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Novel insights into host responses to Japanese Encephalitis Virus infection: Reanalysis of public transcriptome and microRNAome datasets
Abstract
Purpose
Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV), is the principal cause of viral encephalitis in South-East Asian and Western Pacific countries; accounting for 68,000 cases, and up to 20,400 fatalities, annually across the world. Despite being a high-risk condition, there is no specific treatment for JE. Given rapid additions in genomics databases and the power of data reanalysis in addressing critical medical questions, the present study was designed to identify novel host factors that might have potential roles in JEV infection.
Methods
We extracted microarray and RNA-Seq data sets from NCBI-GEO and compared mock and JEV-infected samples. Raw data from all the studies were re-analyzed to identify host factors associated with JEV replication.
Results
We identified several coding and non-coding host factors that had no prior known role in viral infections. Of these, the coding transcripts: Myosin Heavy Chain 10 (MYH10), Progestin and AdipoQ Receptor Family Member 8 (PAQR8), and the microRNAs: hsa-miR-193b-5p, hsa-miR-3714 and hsa-miR-513a-5p were found to be novel host factors deregulated during JEV infection. MYH10 encodes a conventional non-muscle myosin, and mutations in MYH10 have been shown to cause neurological defects. PAQR8 has been associated with epilepsy, which exhibits symptoms similar to JEV infection. JE is a neuro-degenerative disease, and the known involvement of MYH10 and PAQR8 in neurological disorders strongly indicates potential roles of these host factors in JEV infection. Additionally, we observed that MYH10 and PAQR8 had a significant negative correlation with Activating transcription factor 3 (ATF3), which is a previously validated modulator of JEV infection. ATF3 is a transcription factor that binds to the promotors of genes encoding other transcription factors or interferon-stimulated genes and negatively regulates host antiviral responses during JE.
Conclusion
Our findings demonstrate the significance of data reanalysis in the identification of novel host factors that may become targets for diagnosis/ therapy against viral diseases of major concern, such as, JE. The deregulated coding and non-coding transcripts identified in this study need further experimental analysis for validation.
... The actin-myosin network, including myosin VI motor protein (MYO6) (Sun and Whittaker, 2007), dynein, dynactin, and myosin IIB (MYH10) (Banerjee et al., 2014), participates in IAV endocytosis and is also required for proper assembly of influenza virus particles (Kumakura et al., 2015). In particular, MYH10 predominates in neuronal tissue and functions as a host-dependency factor for several neurotropic viruses, such as herpes simplex virus-1 (HSV-1) (Arii et al., 2015 and Japanese encephalitis virus (JEV) (Rajput et al., 2022). In this study, myosin IIA (MYH9) was found to be a key host factor for IAV infection, and either depletion or overexpression of MYH9 causes significant suppression of IAV infection. ...
Influenza A virus (IAV), responsible for seasonal epidemics and recurring pandemics, represents a global threat to public health. Given the risk of a potential IAV pandemic, it is increasingly important to better understand virus-host interactions and develop new anti-viral strategies. Here, we reported nonmuscle myosin IIA (MYH9)-mediated regulation of IAV infection. MYH9 depletion caused a profound inhibition of IAV infection by reducing viral attachment and internalization in human lung epithelial cells. Surprisingly, overexpression of MYH9 also led to a significant reduction in viral productive infection. Interestingly, overexpression of MYH9 retained viral attachment, internalization, or uncoating, but suppressed the viral ribonucleoprotein (vRNP) activity in a minigenome system. Further analyses found that excess MYH9 might interrupt the formation of vRNP by interacting with the viral nucleoprotein (NP) and result in the reduction of the completed vRNP in the nucleus, thereby inhibiting subsequent viral RNA transcription and replication. Together, we discovered that MYH9 can interact with IAV NP protein and engage in the regulation of vRNP complexes, thereby involving viral replication. These findings enlighten new mechanistic insights into the complicated interface of host-IAV interactions, ultimately making it an attractive target for the generation of antiviral drugs.
Background
The emergence of chemoresistance to 5-fluorouracil (5-FU)-based chemotherapy is the main cause of treatment failure in advanced and metastatic colorectal cancer (CRC) patients. Long noncoding RNAs (lncRNAs) have been reported to be involved in 5-FU resistance. Previously, we first detected that lncRNA cetuximab resistance-associated RNA transcript 16 (CRART16) could contribute to cetuximab resistance by upregulating V-Erb-B2 erythroblastic leukemia viral oncogene homologue 3 (ERBB3) expression by sponging miR-371a-5p in CRC cells. The current study aimed to explore the role of CRART16 in acquired 5-FU resistance in CRC cells and its possible mechanism.
Methods
Quantitative real-time PCR (RT-qPCR) was used to measure the expression levels of CRART16 in a 5-FU-resistant CRC cell subline (SW620/5-FU) and the parent cell line. Lentivirus transduction was performed to establish SW620 and Caco-2 cells stably overexpressing CRART16. Cell Counting Kit-8 (CCK-8) assays and colony formation assays were applied to measure cell chemosensitivity to 5-FU. Flow cytometric and immunofluorescence staining were adopted to assess cell apoptosis induced by 5-FU. The dual-luciferase reporter assay was used to validate the direct interactions between CRART16 and miR-193b-5p and between miR-193b-5p and high-mobility group AT-hook-2 (HMGA2). The expression levels of HMGA2, apoptosis-associated proteins and p-ERK were examined by western blotting. The statistical differences within any two groups were used Student’s t test.
Results
CRART16 was upregulated in SW620/5-FU cells. Overexpression of CRART16 reduced the sensitivity of CRC cells to 5-FU by attenuating apoptosis. In addition, CRART16 promoted 5-FU resistance by suppressing the expression of miR-193b-5p. Furthermore, CRART16 modulated the expression of HMGA2 by inhibiting miR-193b-5p and activated the MAPK signaling pathway.
Conclusions
CRART16 confers 5-FU resistance in CRC cells through the CRART16/miR-193b-5p/HMGA2/MAPK pathway.
Breast cancer (BC) is the most commonly occurring malignancy in women. This study aimed to investigate the functions of the long noncoding RNA ZBED3‐AS1 (ZBED3‐AS1) in BC and its molecular mechanisms. qRT‐PCR was conducted to access the expression of ZBED3‐AS1, microRNA‐513a‐5p (miR‐513a‐5p), and Kruppel like factor 6 (KLF6) in BC. Additionally, BC cell viability and proliferative capacity were measured by MTT and 5‐Ethynyl‐20‐deoxyuridine (EdU) assays. A transwell assay was used for evaluating BC cell migration and invasion. The interactions among ZBED3‐AS1, miR‐513a‐5p, and KLF6 in BC were confirmed by dual‐luciferase reporter assay. Furthermore, feedback approaches were performed to determine whether ZBED3‐AS1 influences BC cell behaviors by regulating the miR‐513a‐5p/KLF6 axis. The murine xenograft model was established to assess the effect of ZBED3‐AS1 on tumor growth. The expression of ZBED3‐AS1 and KLF6 was reduced, while miR‐513a‐5p expression was elevated in BC. ZBED3‐AS1 elevation attenuated the malignant behaviors of BC cells, including viability, proliferative capacity, migration, and invasion. Mechanical experiments revealed that ZBED3‐AS1 targeted miR‐513a‐5p, and miR‐513a‐5p targeted KLF6 in BC. Feedback approaches validated that miR‐513a‐5p overexpression or KLF6 depletion reversed the inhibitory effects of ZBED3‐AS1 upregulation on viability, proliferative capacity, migration, and invasion of BC cells. Furthermore, ZBED3‐AS1 elevation attenuated the tumor growth in the murine xenograft model. ZBED3‐AS1 hindered the malignant development of BC cells by regulating the miR‐513a‐5p/KLF6 axis, providing a novel therapeutic target in BC. Diagrammatic sketch of the lncRNA ZBED3‐AS1‐miR‐513‐3p‐KLF6 axis in the breast.
Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tools to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package has been enhanced considerably compared to its original version published nine years ago. The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization. Other new features include gene set enrichment analysis (GSEA) and comparison of enrichment results from multiple gene lists. We anticipate that clusterProfiler 4.0 will be applied in a wide range of scenarios across diverse organisms.
Gastric cancer is one of the leading prevalent and malignant cancers worldwide, especially in east Asia. However, the in-depth molecular mechanism underlying gastric cancer progression remains uncertain. Recently, studies have identified that long non-coding RNA (lncRNA) could play critical roles in the tumorigenesis of multiple types of cancer. Studies on long non-coding RNA BLACAT2 have proven that it participates in bladder cancer and colorectal cancer regulation and was identified as highly expressed using the cBioPortal for Cancer Genomics in gastric cancer. However, the precise function of lncRNA-BLACAT2 in the carcinogenesis and progression of gastric cancer remains largely unexplored. Our study discovered that lncRNA-BLACAT2 was significantly upregulated in gastric cancer. Different studies have illustrated that BLACAT2 promoted gastric cancer progression through regulating proliferation, migration, invasion, and apoptosis in terms of biological function.
Furthermore, BLACAT2 was verified to perform its function through interaction with miR-193b-5p using a luciferase reporter assay. On the other hand, MiR-193b-5p specific inhibitor treatment reversed the inhibitory effect of BLACAT2 on cell biological functions. Additional studies also discovered that Methyltransferase Like 3 (METTL3) was the downstream target of miR-193b-5p. Subsequently, restoration of METTL3 eliminated the suppressive effect of proliferation or the promotive effect of apoptosis caused by BLACAT2 knockdown. To sum up, these experimental results demonstrated that BLACAT2 acted as an oncogene in gastric cancer progression through the regulation of the miR-193b-5p/METTL3 pathway, hence providing new insights regarding the pathogenesis of gastric cancer.
Myosin Va (MyoVa) is a plus-end filamentous-actin motor protein that is highly and broadly expressed in the vertebrate body, including in the nervous system. In excitatory neurons, MyoVa transports cargo toward the tip of the dendritic spine, where the postsynaptic density (PSD) is formed and maintained. MyoVa mutations in humans cause neurologic dysfunction, intellectual disability, hypomelanation, and death in infancy or childhood. Here, we characterize the Flailer (Flr) mutant mouse, which is homozygous for a myo5a mutation that drives high levels of mutant MyoVa (Flr protein) specifically in the CNS. Flr protein functions as a dominant-negative MyoVa, sequestering cargo and blocking its transport to the PSD. Flr mice have early seizures and mild ataxia but mature and breed normally. Flr mice display several abnormal behaviors known to be associated with brain regions that show high expression of Flr protein. Flr mice are defective in the transport of synaptic components to the PSD and in mGluR-dependent long-term depression (LTD) and have a reduced number of mature dendritic spines. The synaptic and behavioral abnormalities of Flr mice result in anxiety and memory deficits similar to that of other mouse mutants with obsessive-compulsive disorder and autism spectrum disorder (ASD). Because of the dominant-negative nature of the Flr protein, the Flr mouse offers a powerful system for the analysis of how the disruption of synaptic transport and lack of LTD can alter synaptic function, development and wiring of the brain and result in symptoms that characterize many neuropsychiatric disorders.
Purpose
Long noncoding RNAs (lncRNAs) exert important functions in the progression of cancers. Currently, we aim to investigate the potential roles of lncRNA ADAM Metallopeptidase with Thrombospondin Type 1 Motif 9 Antisense RNA 1 (ADAMTS9-AS1) in breast carcinoma.
Materials and Methods
The expressions of ADAMTS9-AS1 and miR-513a-5p in breast carcinoma tissues and cell lines were detected using qRT-PCR. Cell Counting Kit-8 (CCK-8) and transwell assays were used to assess the viability and invasive ability of breast cancer cells. The direct interaction between ADAMTS9-AS1 and miR-513a-5p was predicted using bioinformatics tools. The target of miR-513a-5p, ZFP36 Ring Finger Protein (ZFP36) was validated by luciferase assay. The expression of ZFP36 was measured using Western blot assay. Breast cancer MDA-MB-231 cells growth in vivo was evaluated using xenograft tumor assay.
Results
ADAMTS9-AS1 was downregulated in breast cancer tissues as well as cell lines. Upregulation of ADAMTS9-AS1 suppressed the growth and invasiveness of breast carcinoma cells in vitro as well as inhibiting cellgrowth in vivo. Furthermore, ZFP36 was manifested as the target gene of miR-513a-5p and negatively modulated by ADAMTS9-AS1. In addition, overexpression of ADAMTS9-AS1 neutralized the promoting impact of miR-513a-5p on the aggressiveness of breast cancer cells.
Conclusion
In conclusion, lncRNA ADAMTS9-AS1 inhibited the aggressive phenotypes of breast carcinoma cells via sponging miR-513a-5p and regulating ZFP36.
Background:
MicroRNAs (miRNAs) have been found to have functions regulating cell proliferation, differentiation and apoptosis, thereby regulating the occurrence, development and prognosis of tumors. MiR-193b-3p is well-known for its tumorigenic effect, but there are few studies on miR-193b-5p, and its role in tongue cancer has not been reported.
Methods:
In the present research, we investigated the specific role of miR-193b-5p in tongue cancer. MiR-193b-5p mimics were transfected into tongue cancer cell lines CAL27 and TCA-8113 to generate miR-193b-5p overexpression cells. CCK-8, clonogenic assay, wound healing assay, transwell and flow cytometry analysis were performed to detect cell proliferation, migration, invasion and apoptosis.
Results:
Our data showed that the exogenous overexpression of miR-193b-5p blocked the proliferation, inhibited the phosphorylation of AKT and mTOR, and downregulated the levels of Cyclin D1 and P70 of CAL27 and TCA-8113 cells. We predicted that miR-193b-5p suppressed the proliferation of cancer cells by inhibiting the AKT/mTOR pathway. MiR-193b-5p mimics also induced the apoptosis of CAL27 and TCA-8113 cells by inhibiting the expression of Bcl2 and promoting the levels of Active-Caspase3 and Bax. Furthermore, a marked decline in the migration and invasiveness of tongue cancer cells transected with miR-193b-5p mimics was observed. According to the results of western blot, miR-193b-5p downregulated the levels of the epithelial-to-mesenchymal transition (EMT) markers, including N-cad, Vimentin, Snail and Slug, while upregulating E-cad expression level in CAL27 and TCA-8113 cells, suggesting that miR-193b-5p inhibited the migration and invasion by reversing the EMT process. In addition, miR-193b-5p mimics inhibited the formation of clonogenic colonies of CAL27 and TCA-8113 cells after irradiation.
Conclusions:
Taken together, miR-193b-5p mimics block cell proliferation, migration and invasion and induce apoptosis by inhibiting the AKT/mTOR signaling pathway; they also reversed EMT progression and inhibited the radio-resistance of tongue cancer cells. Our results provide a potential target for the clinical treatment of human tongue cancer.
The amount of omics data in the public domain is increasing every year. Modern science has become a data-intensive discipline. Innovative solutions for data management, data sharing, and for discovering novel datasets are therefore increasingly required. In 2016, we released the first version of the Omics Discovery Index (OmicsDI) as a light-weight system to aggregate datasets across multiple public omics data resources. OmicsDI aggregates genomics, transcriptomics, proteomics, metabolomics and multiomics datasets, as well as computational models of biological processes. Here, we propose a set of novel metrics to quantify the attention and impact of biomedical datasets. A complete framework (now integrated into OmicsDI) has been implemented in order to provide and evaluate those metrics. Finally, we propose a set of recommendations for authors, journals and data resources to promote an optimal quantification of the impact of datasets.
Oxaliplatin as a component of (Neo-) adjuvant chemotherapeutic regimens is administered to colorectal cancer patients. Unfortunately, the acquisition of resistance to this drug in nearly 90% of metastatic patients rendered it as an ineffective drug. Therefore, resistance mechanisms to this drug should be elucidated. There are different genes like GSTP1 and ABCB1 which are responsible for oxaliplatin resistance. We hypothesized that miR-129-5p, miR-302c-5p, miR-3664-5p, mir-3714 and miR-513a-3p are targeting ABCB1 gene, while GSTP1 was predicted to be the potential target of miR-3664-5p, mir-3714 and miR-513a-3p. In order to study this hypothesis, resistant colorectal cell lines were generated through intermittent exposure of HCT116, SW480 and HT29 to the increasing doses of oxaliplatin. MTT assays validated this resistance induction. Expression of ABCB1 and GSTP1 in addition to their targeting miRNAs in different cell lines were studied by quantitative real time PCR in the cell lines.
Even though in comparison with HCT116 and SW480 cell lines, GSTP1 expression was reduced in resistant cells, ABCB1 expression was upregulated in these cell lines. On the other hand, HT-29 resistant cells showed elevated GSTP1 and unchanged ABCB1 levels. While miR-302c-5p level was downregulated in resistant cell lines, miR-129-5p and miR-3664-5p level showed different pattern of reduction in the resistant SW480 and HCT116 cell lines. GSTP1 level was correlated directly with miR-513a-3p and miR-3664-5p in all SW480 and HCT116 derived cell lines, however in HT-29-OXR1, GSTP1 level was correlated inversely with miR-3664-5p. In conclusion, upregulation of ABCB1 can be considered as the crucial component of poor response to oxaliplatin which is likely controlled by miR-302c-5p.
Proteins and their functional interactions form the backbone of the cellular machinery. Their connectivity network needs to be considered for the full understanding of biological phenomena, but the available information on protein-protein associations is incomplete and exhibits varying levels of annotation granularity and reliability. The STRING database aims to collect, score and integrate all publicly available sources of protein-protein interaction information, and to complement these with computational predictions. Its goal is to achieve a comprehensive and objective global network, including direct (physical) as well as indirect (functional) interactions. The latest version of STRING (11.0) more than doubles the number of organisms it covers, to 5090. The most important new feature is an option to upload entire, genome-wide datasets as input, allowing users to visualize subsets as interaction networks and to perform gene-set enrichment analysis on the entire input. For the enrichment analysis, STRING implements well-known classification systems such as Gene Ontology and KEGG, but also offers additional, new classification systems based on high-throughput text-mining as well as on a hierarchical clustering of the association network itself. The STRING resource is available online at https://string-db.org/.
miRNAs are crucially involved in cellular responses to exotic chemical toxins. However, the role of miRNAs in organophosphates induced cytotoxicity is poorly understood. In present study, we investigated the role of miR-513a-5p in dichlorvos induced cytotoxicity in human kidney cell line HK-2. We found that dichlorvos increased intracellular ROS level, upregulated miR-513a-5p expression and induced apoptosis in HK-2 cells. Moreover, overexpression of miR-513a-5p promoted apoptosis of HK-2 cells with or without exposure to dichlorvos while anti-miR-513a-5p partially suppressed dichlorvos induced apoptosis. Luciferase assay showed that miR-513a-5p could directly bind to the 3'-untranslated regions of Bcl-2. Furthermore, miR-513a-5p decreased the level of Bcl-2 and promoted dichlorvos induced apoptosis in HK-2 cells through the Bcl-2/Bax-Caspase-3 pathway. Taken together, our findings indicate that miR-513a-5p promotes dichlorvos induced apoptosis by targeting Bcl-2.
Purpose
Given the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.
Methods
We tested this hypothesis in the United Kingdom–wide Deciphering Developmental Disorders study, where in 2014 we reported a diagnostic yield of 27% through whole-exome sequencing of 1,133 children with severe developmental disorders and their parents. We reanalyzed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes.
Results
We are now able to diagnose an additional 182 individuals, taking our overall diagnostic yield to 454/1,133 (40%), and another 43 (4%) have a finding of uncertain clinical significance. The majority of these new diagnoses are due to novel developmental disorder–associated genes discovered since our original publication.
Conclusion
This study highlights the importance of coupling large-scale research with clinical practice, and of discussing the possibility of iterative reanalysis and recontact with patients and health professionals at an early stage. We estimate that implementing parent–offspring whole-exome sequencing as a first-line diagnostic test for developmental disorders would diagnose >50% of patients.
MicroRNAs are important regulators of gene expression, achieved by binding to the gene to be regulated. Even with modern high-throughput technologies, it is laborious and expensive to detect all possible microRNA targets. For this reason, several computational microRNA-target prediction tools have been developed, each with its own strengths and limitations. Integration of different tools has been a successful approach to minimize the shortcomings of individual databases. Here, we present mirDIP v4.1, providing nearly 152 million human microRNA-target predictions, which were collected across 30 different resources. We also introduce an integrative score, which was statistically inferred from the obtained predictions, and was assigned to each unique microRNA-target interaction to provide a unified measure of confidence. We demonstrate that integrating predictions across multiple resources does not cumulate prediction bias toward biological processes or pathways. mirDIP v4.1 is freely available at http://ophid.utoronto.ca/mirDIP/.
MicroRNAs (miRNAs) might be considered both predictors and players of cancer development. The aim of the present report was to investigate whether many years before the diagnosis of breast cancer miRNA expression is already disregulated. In order to test this hypothesis we compared miRNAs extracted from leukocytes in healthy women who later developed breast cancer and in women who remain healthy during the whole fifteen-year follow-up time. Accordantly, we used a case-control study design nested in the ORDET prospective cohort study addressing the possibility that miRNAs can serve as both early biomarkers and components of the hormonal etiological pathways leading to breast cancer development in premenopausal women. We compared leukocyte miRNA profiles of 191 incident premenopausal breast cancer cases and profiles of 191 women who remained healthy over a follow-up period of 20 years. The analysis identified 20 differentially expressed miRNAs in women candidate to develop breast cancer versus control women. The up-regulated miRNAs, miR-513-a-5p, miR-513b-5p and miR-513c-5p were among the most significantly deregulated miRNAs. In multivariate analysis, miR-513a-5p up-regulation was directly and statistically significant associated with breast cancer risk (OR=1.69; 95% CI, 1.08 to 2.64; P=0.0293). In addition, the up-regulation of miR-513-a-5p displayed the strongest direct association with serum progesterone and testosterone levels. The experimental data corroborated the inhibitory function of miR-513a-5p on progesterone receptor expression confirming that progesterone receptor is a target of miR-513a-5p.The identification of up-regulated miR-513a-5p with its oncogenic potential further validates the use of miRNAs as long-term biomarker of breast cancer risk.
Stringent regulation of antiviral signaling and cellular autophagy is critical for the host response to virus infection. However, little is known how these cellular processes are regulated in the absence of type I interferon signaling. Here, we show that ATF3 is induced following Japanese encephalitis virus (JEV) infection, and regulates cellular antiviral and autophagy pathways in the absence of type I interferons in mouse neuronal cells. We have identified new targets of ATF3 and show that it binds to the promoter regions of Stat1, Irf9, Isg15 and Atg5 thereby inhibiting cellular antiviral signaling and autophagy. Consistent with these observations, ATF3-depleted cells showed enhanced antiviral responses and induction of robust autophagy. Furthermore, we show that JEV replication was significantly reduced in ATF3-depleted cells. Our findings identify ATF3 as a negative regulator of antiviral signaling and cellular autophagy in mammalian cells, and demonstrate its important role in JEV life cycle.
Mx proteins are interferon (IFN)-induced dynamin-like GTPases that are present in all vertebrates and inhibit the replication of myriad viruses. However, the role Mx proteins play in IFN-mediated suppression of Japanese encephalitis virus (JEV) infection is unknown. In this study, we set out to investigate the effects of Mx1 and Mx2 expression on the interferon-α (IFNα) restriction of JEV replication. To evaluate whether the inhibitory activity of IFNα on JEV is dependent on Mx1 or Mx2, we knocked down Mx1 or Mx2 with siRNA in IFNα-treated PK-15 cells and BHK-21 cells, then challenged them with JEV; the production of progeny virus was assessed by plaque assay, RT-qPCR, and Western blotting. Our results demonstrated that depletion of Mx1 or Mx2 did not affect JEV restriction imposed by IFNα, although these two proteins were knocked down 66% and 79%, respectively. Accordingly, expression of exogenous Mx1 or Mx2 did not change the inhibitory activity of IFNα to JEV. In addition, even though virus-induced membranes were damaged by Brefeldin A (BFA), overexpressing porcine Mx1 or Mx2 did not inhibit JEV proliferation. We found that BFA inhibited JEV replication, not maturation, suggesting that BFA could be developed into a novel antiviral reagent. Collectively, our findings demonstrate that IFNα inhibits JEV infection by Mx-independent pathways.
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.
Radiotherapy in osteosarcoma patients is problematic due to radioresistance; therefore, understanding the mechanism of radioresistance is integral to providing effective radiotherapeutic regimens for osteosarcoma. We now report the activity of an miRNA, miR-513a-5p, in stimulating radiosensitivity of osteosarcoma cells in vitro and in vivo. MiR-513a-5p expression is decreased in osteosarcoma tissue from patients and cultured osteosarcoma cell lines. However, exogenous re-expression of this miRNA in osteosarcoma cell lines, including HOS, U2OS and 9901, can induce sensitization to ionizing radiation. We also confirm that miR-513a-5p suppresses APE1 expression, and that both the redox and DNA repair activity of APE1 were decreased in miR-513a-5p expressing cell lines. By suppressing APE1, miR-513a-5p induces the DNA damage response which stimulates apoptosis after irradiation. Our report establishes miR-513a-5p as a radiosensitizing miRNA and identifies its activity in the suppression of APE1, which could directly lead to radiosensitization.
Cytokines and IFNs downstream of innate immune pathways are critical for mounting an appropriate immune response to microbial infection. However, the expression of these inflammatory mediators is tightly regulated, as uncontrolled production can result in tissue damage and lead to chronic inflammatory conditions and autoimmune diseases. Activating transcription factor 3 (ATF3) is an important transcriptional modulator that limits the inflammatory response by controlling the expression of a number of cytokines and chemokines. However, its role in modulating IFN responses remains poorly defined. In this study, we demonstrate that ATF3 expression in macrophages is necessary for governing basal IFN-β expression, as well as the magnitude of IFN-β cytokine production following activation of innate immune receptors. We found that ATF3 acted as a transcriptional repressor and regulated IFN-β via direct binding to a previously unidentified specific regulatory site distal to the Ifnb1 promoter. Additionally, we observed that ATF3 itself is a type I IFN-inducible gene, and that ATF3 further modulates the expression of a subset of inflammatory genes downstream of IFN signaling, suggesting it constitutes a key component of an IFN negative feedback loop. Consistent with this, macrophages deficient in Atf3 showed enhanced viral clearance in lymphocytic choriomeningitis virus and vesicular stomatitis virus infection models. Our study therefore demonstrates an important role for ATF3 in modulating IFN responses in macrophages by controlling basal and inducible levels of IFNβ, as well as the expression of genes downstream of IFN signaling.
Background:
Systematic analysis of cancer gene-expression patterns using high-throughput transcriptional profiling technologies has led to the discovery and publication of hundreds of gene-expression signatures. However, few public signature values have been cross-validated over multiple studies for the prediction of cancer prognosis and chemosensitivity in the neoadjuvant setting.
Methods:
To analyze the prognostic and predictive values of publicly available signatures, we have implemented a systematic method for high-throughput and efficient validation of a large number of datasets and gene-expression signatures. Using this method, we performed a meta-analysis including 351 publicly available signatures, 37,000 random signatures, and 31 breast cancer datasets. Survival analyses and pathologic responses were used to assess prediction of prognosis, chemoresponsiveness, and chemo-drug sensitivity.
Results:
Among 31 breast cancer datasets and 351 public signatures, we identified 22 validation datasets, two robust prognostic signatures (BRmet50 and PMID18271932Sig33) in breast cancer and one signature (PMID20813035Sig137) specific for prognosis prediction in patients with ER-negative tumors. The 22 validation datasets demonstrated enhanced ability to distinguish cancer gene profiles from random gene profiles. Both prognostic signatures are composed of genes associated with TP53 mutations and were able to stratify the good and poor prognostic groups successfully in 82%and 68% of the 22 validation datasets, respectively. We then assessed the abilities of the two signatures to predict treatment responses of breast cancer patients treated with commonly used chemotherapeutic regimens. Both BRmet50 and PMID18271932Sig33 retrospectively identified those patients with an insensitive response to neoadjuvant chemotherapy (mean positive predictive values 85%-88%). Among those patients predicted to be treatment sensitive, distant relapse-free survival (DRFS) was improved (negative predictive values 87%-88%). BRmet50 was further shown to prospectively predict taxane-anthracycline sensitivity in patients with HER2-negative (HER2-) breast cancer.
Conclusions:
We have developed and applied a high-throughput screening method for public cancer signature validation. Using this method, we identified appropriate datasets for cross-validation and two robust signatures that differentiate TP53 mutation status and have prognostic and predictive value for breast cancer patients.
Viperin is identified as an antiviral protein induced by interferon (IFN), viral infections, and pathogen-associated molecules.
In this study, we found that viperin is highly induced at the RNA level by Japanese encephalitis virus (JEV) and Sindbis virus
(SIN) and that viperin protein is degraded in JEV-infected cells through a proteasome-dependent mechanism. Promoter analysis
revealed that SIN induces viperin expression in an IFN-dependent manner but that JEV by itself activates the viperin promoter
through IFN regulatory factor-3 and AP-1. The overexpression of viperin significantly decreased the production of SIN, but
not of JEV, whereas the proteasome inhibitor MG132 sustained the protein level and antiviral effect of viperin in JEV-infected
cells. Knockdown of viperin expression by RNA interference also enhanced the replication of SIN, but not that of JEV. Our
results suggest that even though viperin gene expression is highly induced by JEV, it is negatively regulated at the protein
level to counteract its antiviral effect. In contrast, SIN induces viperin through the action of IFN, and viperin exhibits
potent antiviral activity against SIN.
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
The innate immune system senses viral infection by recognizing a variety of viral components (including double-stranded (ds)RNA) and triggers antiviral responses. The cytoplasmic helicase proteins RIG-I (retinoic-acid-inducible protein I, also known as Ddx58) and MDA5 (melanoma-differentiation-associated gene 5, also known as Ifih1 or Helicard) have been implicated in viral dsRNA recognition. In vitro studies suggest that both RIG-I and MDA5 detect RNA viruses and polyinosine-polycytidylic acid (poly(I:C)), a synthetic dsRNA analogue. Although a critical role for RIG-I in the recognition of several RNA viruses has been clarified, the functional role of MDA5 and the relationship between these dsRNA detectors in vivo are yet to be determined. Here we use mice deficient in MDA5 (MDA5-/-) to show that MDA5 and RIG-I recognize different types of dsRNAs: MDA5 recognizes poly(I:C), and RIG-I detects in vitro transcribed dsRNAs. RNA viruses are also differentially recognized by RIG-I and MDA5. We find that RIG-I is essential for the production of interferons in response to RNA viruses including paramyxoviruses, influenza virus and Japanese encephalitis virus, whereas MDA5 is critical for picornavirus detection. Furthermore, RIG-I-/- and MDA5-/- mice are highly susceptible to infection with these respective RNA viruses compared to control mice. Together, our data show that RIG-I and MDA5 distinguish different RNA viruses and are critical for host antiviral responses.
Japanese encephalitis virus (JEV) is a flavivirus, spread by the bite of carrier Culex mosquitoes. The subsequent disease caused is Japanese encephalitis (JE), which is the leading global cause of virus-induced encephalitis. The disease is predominant in the entire Asia-Pacific region with the potential of global spread. JEV is highly neuroinvasive with symptoms ranging from mild fever to severe encephalitis and death. One-third of JE infections are fatal, and half of the survivors develop permanent neurological sequelae. Disease prognosis is determined by a series of complex and intertwined signaling events dictated both by the virus and the host. All flaviviruses, including JEV replicate in close association with ER derived membranes by channelizing the protein and lipid components of the ER. This leads to activation of acute stress responses in the infected cell-oxidative stress, ER stress, and autophagy. The host innate immune and inflammatory responses also enter the fray, the components of which are inextricably linked to the cellular stress responses. These are especially crucial in the periphery for dendritic cell maturation and establishment of adaptive immunity. The pathogenesis of JEV is a combination of direct virus induced neuronal cell death and an uncontrolled neuroinflammatory response. Here we provide a comprehensive review of the JEV life cycle and how the cellular stress responses dictate the pathobiology and resulting immune response. We also deliberate on how modulation of these stress pathways could be a potential strategy to develop therapeutic interventions, and define the persisting challenges.
Studies have demonstrated that both mortality and severe illness rates exist significant difference in different gender COVID-19 patients, but the reasons are still very mysterious to date. Here, we firstly find that the survival outcome of female patients is better to male patients through analyzing the 3044 COVID-19 cases. Secondly, we identify many important master regulators [e.g. STAT1/STAT2 and zinc finger (ZNF) proteins], in particular female patients can express more ZNF proteins and stronger transcriptional activities than male patients in response to SARS-CoV-2 infection. Thirdly, we discover that ZNF protein activity is significantly negative correlation with the SARS-CoV-2 load of COVID-19 patients, and ZNF proteins as transcription factors can also activate their target genes to participate in anti-SARS-CoV-2 infection. Fourthly, we demonstrate that ZNF protein activity is positive correlation with the abundance of multiple immune cells of COVID-19 patients, implying that the highly ZNF protein activity might promote the abundance and the antiviral activity of multiple immune cells to effectively suppress SARS-CoV-2 infection. Taken together, our study proposes an underlying anti-SARS-COV-2 role of ZNF proteins, and differences in the amount and activity of ZNF proteins might be responsible for the distinct prognosis of different gender COVID-19 patients.
Acrylamide (AA), an important by-product of the Maillard reaction, has been reported to be genotoxic and carcinogenic. The present study employed miRNAs to investigate the toxic mechanism of AA and their role against AA toxicity. Deep sequencing of small RNA libraries was performed and miR-193b-5p was applied for further study. AA significantly reduced the level of miR-193b-5p and its ectopic expression promoted cell cycle G1/S transition and cell proliferation by upregulating the cyclin-dependent kinase regulator Cyclin D1 and downregulating the cyclin-dependent kinase inhibitor p21, while miR-193b-5p inhibitor led to the opposite results. Dual luciferase assay demonstrated miR-193b-5p regulated the expression of FoxO3 by directly targeting the FoxO3 3′-untranslated region (3′-UTR). Knockdown of FoxO3 induced cell cycle G1/S transition and cell proliferation, which was suppressed by the inhibition of miR-193b-5p but promoted by miR-193b-5p mimics. MiR-193b-5p inhibitor strengthened the effect of FoxO3, contrary to the effect of miR-193b-5p mimics. In conclusion, miR-193b-5p acted as a regulator of cell cycle G1/S transition and cell proliferation by targeting FoxO3 to mediate the expression of p21 and Cyclin D1.
There is increasing evidence regarding the pivotal roles of microRNAs (miRNAs) and histone deacetylases (HDACs) in the development of osteoarthritis (OA). This study aimed to determine whether miR‐193b‐5p regulates HDAC7 expression directly to affect cartilage degeneration. Expression levels of miR‐193b‐5p, HDAC7, matrix metalloproteinase 3 (MMP3), and MMP13 were determined in normal and OA cartilage and primary human chondrocytes (PHCs) stimulated with interleukin‐1β (IL‐1β). PHCs were transfected with a miR‐193b‐5p mimic or inhibitor to verify whether miR‐193b‐5p influences the expression of HDAC7 and MMPs. A luciferase reporter assay was performed to demonstrate the binding between miR‐193b‐5p and the 3′‐untranslated region (UTR) of HDAC7. Expression of miR‐193b‐5p was reduced in IL‐1β‐stimulated PHCs and in OA cartilage compared to that in normal cartilage. Luciferase reporter assay exhibited the repressed activity of the reporter construct containing the 3′UTR of HDAC7. Both miR‐193b‐5p overexpression and HDAC7 inhibition decreased the expression of MMP3 and MMP13, whereas the inhibition of miR‐193b‐5p enhanced HDAC7, MMP3, and MMP13 expression. miR‐193b‐5p downregulates HDAC7 directly and, as a result, inhibits MMP3 and MMP13 expression, which suggests that miR‐193b‐5p has a protective role in OA.
Japanese encephalitis virus (JEV) causes central nervous system neuronal injury and inflammation. A clear understanding of neuronal responses to JEV infection remains elusive. Using the Affymetrix array to investigate the transcriptome of infected SK-N-MC cells, 1316 and 2737 dysregulated genes (≥ 2/−2 fold change, P < 0.05) were found at 48 hours post-infection (hpi) and 60 hpi, respectively. The genes were mainly involved in anti-microbial responses, cell signalling, cellular function and maintenance, and cell death and survival. Among the most highly upregulated genes (≥ 10 folds, P < 0.05) were chemokines CCL5, CXCL11, IL8 and CXCL10. The upregulation and expression of CXCL11 were confirmed by qRT-PCR and immunofluorescence. Pathogen recognition receptors retinoic acid-inducible gene-1 (RIG-1) and melanoma differentiation-associated protein 5 (MDA5) were also upregulated. Our results strongly suggest that neuronal cells play a significant role in immunity against JEV. CXCL11, RIG-1 and MDA5 and other cytokines may be important in neuropathogenesis.
Quercetin (3,3′,4′,5,7-pentahydroxyflavone) is a major dietary flavonol found in diverse fruits and vegetables such as onions, cauliflower, apple skin, lettuce and chili peppers. In recent studies, quercetin is reported as a functional compound and shows a wide range of biological effects such as antioxidant, anti-inflammatory and antiangiogenic properties in obesity, diabetes, cardiovascular diseases and various cancers. However, to date, the therapeutic effect of quercetin on the progression of endometriosis, which is a common gynecological disease in reproductive-aged women and brings chronic pelvic pain and infertility, has not been examined in depth. Results of this study demonstrated that quercetin inhibited the proliferation and induced the cell cycle arrest in VK2/E6E7 and End1/E6E7 cells. Furthermore, it induced cell apoptosis with DNA fragmentation, loss of mitochondrial membrane potential and reactive oxygen species production. The effects accompanied down-regulation of ERK1/2, P38 MAPK and AKT signaling molecules. Additionally, the administration of quercetin indicated antiproliferative and anti-inflammatory effects on endometriosis autoimplanted mouse models. The mRNA expression of Ccnd1 significantly decreased in response to quercetin intraperitoneal injection when compared to that in vehicle-treated mice. The knockdown of CCND1 mRNA attenuated the proliferation with sub-G0/G1 cell cycle arrest and increased the apoptosis of VK2/E6E7 and End1/E6E7 cells. Furthermore, the treatment of quercetin induced miR-503-5p, miR-1283, miR-3714 and miR-6867-5p related to CCND1 in both cell lines and also stimulated miR-503-5p and miR-546 expression in the mouse model. Hence, quercetin may potentially act as a natural therapeutic to reduce and treat human endometriosis.
Japanese encephalitis is a severe disease caused by Japanese encephalitis virus, genus Flavivirus, family Flaviviridae, which is endemic to most of rural Asia and for which no specific treatment exists.
Japanese encephalitis causes loss of more disability-adjusted life years than any other arthropod-borne virus owing to the frequent neurological sequelae of the condition.
Pathogenesis studies indicate that inhibition of viral replication, viral spread and the host response are needed in combination for optimal therapy.
Animal models and in vitro experiments highlight a number of compounds that are potentially suitable for treatment of Japanese encephalitis in humans that could be tested without delay.
The minimum clinically significant treatment effect has probably been underestimated, and previous clinical trials of Japanese encephalitis have been too small; larger, pragmatic trials are needed.
-The three isoforms of nonmuscle myosin II (NMII-A, NMII-B and NMII-C) play various roles during mouse embryonic development. Previous work, using knockout and hypomorphic mice, showed that MYH10 encoding myosin heavy chain II-B is critical for cardiac and brain development. Ablating or decreasing NMII-B by 80% results in cardiac (ventricular septal defect, double outlet of the right ventricle) and brain defects but not midline fusion defects. Neither NMII-A nor II-C appear to play roles in early myocardial development.
-We had previously generated point mutant knock-in mice and now report novel findings due to expressing motor deficient NMII-B at wild-type levels. Homozygous mice die at E14.5 in cardiac failure exhibiting abnormalities not seen in NMII-B null and hypomorphic mice: a failure in midline fusion resulting in a cleft palate, ectopia cordis, and a large omphalocele. Fusion of the sternum and endocardial cushions is impaired in the mutant mice associated with a failure in apoptosis of the mesenchyme cells. Failure to disassemble myocyte cell-cell adhesions during cardiac outflow tract development contributes to impaired outflow tract myocardialization and displacement of the aorta to the right ventricle.
-Expression of motor impaired NMII-B disrupts normal ventral body wall closure, due to a dominant negative effect. This is not due to the loss of NMII-B function but rather to a gain-of-function resulting from prolonged crosslinking of NMII-B to actin-filaments thereby interfering with the dynamics of actomyosin cytoskeletal structure. Moreover impaired NMII-B motor activity inhibits outflow tract myocardialization leading to mis-localization of the aorta.
Interferons (IFN) are essential antiviral cytokines that establish the cellular antiviral state through upregulation of hundreds of interferon-stimulated genes (ISGs), most of which have uncharacterized functions and mechanisms. We identified cholesterol-25-hydroxylase (CH25H) as a broadly antiviral ISG. CH25H converts cholesterol to a soluble antiviral factor, 25-hydroxycholesterol (25HC). 25HC treatment in cultured cells broadly inhibited growth of enveloped viruses including VSV, HSV, HIV, and MHV68 and acutely pathogenic EBOV, RVFV, RSSEV, and Nipah viruses under BSL4 conditions. It suppressed viral growth by blocking membrane fusion between virus and cell. In animal models, Ch25h-deficient mice were more susceptible to MHV68 lytic infection. Moreover, administration of 25HC in humanized mice suppressed HIV replication and reversed T cell depletion. Thus, our studies demonstrate a unique mechanism by which IFN achieves its antiviral state through the production of a natural oxysterol to inhibit viral entry and implicate membrane-modifying oxysterols as potential antiviral therapeutics.
Astrocytes are the most numerous cell type within the central nervous system (CNS) and perform a variety of tasks, from axon guidance and synaptic support, to the control of the blood brain barrier and blood flow. To perform these roles, there is a great variety of astrocytes. In this review, we summarize the function of astrocytes, in particular, their role in maintaining homeostasis at the synapse, regulating neuronal signaling, protecting neurons from oxidative damage, and determining the fate of endogenous neural precursors. The review also highlights recent developments indicating the role of astrocytes in motor neuron disease (MND), emphasizing their potential as therapeutic targets and agents in cell replacement therapy. The Cu-Zn superoxide dismutase (SOD1) gene that has been implicated in 20% of cases of familial MND must be expressed in the glial cells as well as motor neurons to produce the disease state in murine models of disease. Selectively reducing mutant SOD1 (mSOD1) in astrocytes does not affect disease onset but slows disease progression, whereas reducing mSOD1 in motor neurons delays disease onset and slows early disease but has less effect on life span. This suggests that glial cells represent potential therapeutic targets in MND. However, the lack of specific markers for astrocytes, their precursors, and sub-types means that our knowledge of astrocyte development/differentiation and response to injury lags far behind our understanding of function. Only by filling this knowledge gap can astrocytes be effectively targeted or replaced to successfully treat chronic CNS disorders such as MND.
Chemokines and their receptors are important elements for the selective attraction and activation of various subsets of leukocytes. Interferon-gamma inducible protein (IP-10 or CXCL-10) is a potent chemoattractant and has been suggested to enhance the severity of virus infection and neuronal injury. In order to assess functional importance of this chemokine in viral encephalitis, we have exploited an experimental model of Japanese encephalitis. We report for the first time that in Japanese encephalitis, astrocytes are the predominant source of IP-10. A progressive increase in IP-10 induction following viral infection is concomitant with the increase in IFN-gamma a known inducer of IP-10. However, this increase in IFN-gamma level is not sufficient to confer protection as animals eventually succumb to the infection.