Proteomics reveal energy metabolism and mitogen-activated protein kinase signal transduction perturbation in human Borna disease virus Hu-H1-infected oligodendroglial cells

Exploring New Mechanism of Depression from the Effects of Virus on Nerve Cells

Depression is a common neuropsychiatric disorder with long-term recurrent depressed mood, pain and despair, pessimism and anxiety, and even suicidal tendencies as the main symptoms. Depression usually induces or aggravates the development of other related diseases, such as sleep disorders and endocrine disorders. In today's society, the incidence of depression is increasing worldwide, and its pathogenesis is complex and generally believed to be related to genetic, psychological, environmental, and biological factors. Current studies have shown the key role of glial cells in the development of depression, and it is noteworthy that some recent evidence suggests that the development of depression may be closely related to viral infections, such as SARS-CoV-2, BoDV-1, ZIKV, HIV, and HHV6, which infect the organism and cause some degree of glial cells, such as astrocytes, oligodendrocytes, and microglia. This can affect the transmission of related proteins, neurotransmitters, and cytokines, which in turn leads to neuroinflammation and depression. Based on the close relationship between viruses and depression, this paper provides an in-depth analysis of the new mechanism of virus-induced depression, which is expected to provide a new perspective on the mechanism of depression and a new idea for the diagnosis of depression in the future.

ROCK1/MLC2 inhibition induces decay of viral mRNA in BPXV infected cells

Rho-associated coiled-coil containing protein kinase 1 (ROCK1) intracellular cell signaling pathway regulates cell morphology, polarity, and cytoskeletal remodeling. We observed the activation of ROCK1/myosin light chain (MLC2) signaling pathway in buffalopox virus (BPXV) infected Vero cells. ROCK1 depletion by siRNA and specific small molecule chemical inhibitors (Thiazovivin and Y27632) resulted in a reduced BPXV replication, as evidenced by reductions in viral mRNA/protein synthesis, genome copy numbers and progeny virus particles. Further, we demonstrated that ROCK1 inhibition promotes deadenylation of viral mRNA (mRNA decay), mediated via inhibiting interaction with PABP [(poly(A)-binding protein] and enhancing the expression of CCR4-NOT (a multi-protein complex that plays an important role in deadenylation of mRNA). In addition, ROCK1/MLC2 mediated cell contraction, and perinuclear accumulation of p-MLC2 was shown to positively correlate with viral mRNA/protein synthesis. Finally, it was demonstrated that the long-term sequential passage (P = 50) of BPXV in the presence of Thiazovivin does not select for any drug-resistant virus variants. In conclusion, ROCK1/MLC2 cell signaling pathway facilitates BPXV replication by preventing viral mRNA decay and that the inhibitors targeting this pathway may have novel therapeutic effects against buffalopox.

Transcriptome Analysis of Duck and Chicken Brains Infected with Aquatic Bird Bornavirus-1 (ABBV-1)

Aquatic bird bornavirus 1 (ABBV-1) is a neurotropic virus that infects waterfowls, resulting in persistent infection. Experimental infection showed that both Muscovy ducks and chickens support persistent ABBV-1 infection in the central nervous system (CNS), up to 12 weeks post-infection (wpi), without the development of clinical disease. The aim of the present study was to describe the transcriptomic profiles in the brains of experimentally infected Muscovy ducks and chickens infected with ABBV-1 at 4 and 12 wpi. Transcribed RNA was sequenced by next-generation sequencing and analyzed by principal component analysis (PCA) and differential gene expression. The functional annotation of differentially expressed genes was evaluated by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The PCA showed that the infected ducks sampled at both 4 and 12 wpi clustered separately from the controls, while only the samples from the chickens at 12 wpi, but not at 4 wpi, formed a separate cluster. In the ducks, more genes were differentially expressed at 4 wpi than 12 wpi, and the majority of the highly differentially expressed genes (DEG) were upregulated. On the other hand, the infected chickens had fewer DEGs at 4 wpi than at 12 wpi, and the majority of those with high numbers of DEGs were downregulated at 4 wpi and upregulated at 12 wpi. The functional annotation showed that the most enriched GO terms were immune-associated in both species; however, the terms associated with the innate immune response were predominantly enriched in the ducks, whereas the chickens had enrichment of both the innate and adaptive immune response. Immune-associated pathways were also enriched according to the KEGG pathway analysis in both species. Overall, the transcriptomic analysis of the duck and chicken brains showed that the main biological responses to ABBV-1 infection were immune-associated and corresponded with the levels of inflammation in the CNS.

Alterations of the Gut Microbiota in Response to Total Sleep Deprivation and Recovery Sleep in Rats

INTRODUCTION

Accumulating evidence suggests that both sleep loss and gut dysbiosis can lead to metabolic disorders. However, less is known about the impact of total sleep deprivation (SD) and sleep recovery on the composition, function, and metabolic dynamics of the gut microbiota.

METHODS

Specific-pathogen free Sprague-Dawley rats were subjected to 48 h of SD with gentle handling and then allowed to recover for 1 week. Taxonomic profiles of fecal microbiota were obtained at baseline, 24 h of SD, 48 h of SD, and 1 week of recovery. We used 16S rRNA gene sequencing to analyze the gut microbial composition and function and further characterize microbiota-derived metabolites in rats.

RESULTS

The microbiota composition analysis revealed that gut microbial composition and metabolites did not change in the rats after 24 h of SD but were significantly altered after 48 h of SD. These changes were reversible after 1 week of sleep recovery. A functional analysis was performed based on Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, indicating that 19 KEGG pathways were significantly altered in the gut microbiota in SD rats. These functional changes occurred within 24 h of SD, were more apparent after 48 h of SD, and did not fully recover after 1 week of sleep recovery.

CONCLUSION

These results indicate that acute total SD leads to significant compositional and functional changes in the gut microbiota, and these changes are reversible.

miR-505 inhibits replication of Borna disease virus 1 via inhibition of HMGB1-mediated autophagy

Borna disease virus 1 (BoDV-1) is a highly neurotropic RNA virus which was recently demonstrated to cause deadly human encephalitis. Viruses can modulate microRNA expression, in turn modulating cellular immune responses and regulating viral replication. A previous study indicated that BoDV-1 infection down-regulated the expression of miR-505 in rats. However, the underlying mechanism of miR-505 during BoDV-1 infection remains unknown. In this study, we found that miR-505 can inhibit autophagy activation by down-regulating the expression of its target gene HMGB1, and ultimately inhibit the replication of BoDV-1. Specifically, we found that the expression of miR-505 was significantly down-regulated in rat primary neurons stably infected with BoDV-1. Overexpression of miR-505 can inhibit the replication of BoDV-1 in cells. Bioinformatics analysis and dual luciferase reporter gene detection confirmed that during BoDV-1 infection, the high-mobility group protein B1 (HMGB1) that mediates autophagy is the direct target gene of miR-505. The expression of HMGB1 was up-regulated after BoDV-1 infection, and overexpression of miR-505 could inhibit the expression of HMGB1. Autophagy-related detection found that after infection with BoDV-1, the expression of autophagy-related proteins and autophagy-related marker LC3 in neuronal cells was significantly up-regulated. Autophagy flow experiments and transmission electron microscopy also further confirmed that BoDV-1 infection activated HMGB1-mediated autophagy. Further regulating the expression of miR-505 found that overexpression of miR-505 significantly inhibited HMGB1-mediated autophagy. The discovery of this mechanism may provide new ideas and directions for the prevention and treatment of BoDV-1 infection in the future.

Downregulation of SOCS gene expression can inhibit the formation of acute and persistent BDV infections

High expression of suppressors of cytokine signalling (SOCS) has been detected during various viral infections. As a negative feedback regulator, SOCS participates in the regulation of multiple signalling pathways. In this study, to study the related mechanism between SOCS and BDV and to explore the effect of SOCS on IFN pathways in nerve cells, downregulated of SOCS1/3 in oligodendroglial (OL) cells and OL cells persistently infected with BDV (OL/BDV) were constructed with RNA interference technology. An interferon inducer (poly I:C, PIC) and an IFN-α/β R1 antibody were used as stimulation in the SOCS1/3 low-expression cell models, qRT-PCR was used to detect type I IFN and BDV nucleic acid expression, Western blot was used to detect the expression of BDV P40 protein. After BDV acute infection with OL cells which with downregulated SOCS expression, the virus accounting was not detected, and the viral protein expression was lower than that of OL/BDV cells; the OL/BDV cells with downregulated SOCS expression had lower virus nucleic acid and protein expression than OL/BDV cells. Stimulated by IFN-α/β R1 antibody, the expression of type I interferon in OL/BDV cells decreased, and the content of BDV nucleic acid and protein increased, which was higher than that of OL/BDV cells. From the results, it was concluded that downregulating SOCS1/3 can inhibit the formation of acute BDV infection and virus replication in persistent BDV infection by promoting the expression of IFN-α/β and that SOCS can be used as a new target for antiviral therapy.

Host-Directed Antiviral Therapy

Antiviral drugs have traditionally been developed by directly targeting essential viral components. However, this strategy often fails due to the rapid generation of drug-resistant viruses. Recent genome-wide approaches, such as those employing small interfering RNA (siRNA) or clustered regularly interspaced short palindromic repeats (CRISPR) or those using small molecule chemical inhibitors targeting the cellular "kinome," have been used successfully to identify cellular factors that can support virus replication. Since some of these cellular factors are critical for virus replication, but are dispensable for the host, they can serve as novel targets for antiviral drug development. In addition, potentiation of immune responses, regulation of cytokine storms, and modulation of epigenetic changes upon virus infections are also feasible approaches to control infections. Because it is less likely that viruses will mutate to replace missing cellular functions, the chance of generating drug-resistant mutants with host-targeted inhibitor approaches is minimized. However, drug resistance against some host-directed agents can, in fact, occur under certain circumstances, such as long-term selection pressure of a host-directed antiviral agent that can allow the virus the opportunity to adapt to use an alternate host factor or to alter its affinity toward the target that confers resistance. This review describes novel approaches for antiviral drug development with a focus on host-directed therapies and the potential mechanisms that may account for the acquisition of antiviral drug resistance against host-directed agents.

Activation of ERK/CREB/BDNF pathway involved in abnormal behavior of neonatally Borna virus-infected rats

BACKGROUND

Neuropsychiatric disorders are devastating illnesses worldwide; however, the potential involvement of viruses in the pathophysiological mechanisms of psychiatric diseases have not been clearly elucidated. Borna disease virus (BDV) is a neurotropic, noncytopathic RNA virus.

MATERIALS AND METHODS

In this study, we infected neonatal rats intracranially with BDV Hu-H1 and Strain V within 24 hours of birth. Psychological phenotypes were assessed using sucrose preference test, open field test, elevated plus maze test, and forced swim test. The protein expression of ERK/CREB/BDNF pathway was assessed by Western blotting of in vitro and in vivo samples.

RESULTS

Hu-H1-infected rats showed anxiety-like behavior 8 weeks postinfection while Strain V-infected rats demonstrated a certain abnormal behavior. Phosphorylated ERK1/2 was significantly upregulated in the hippocampi of Strain V- and Hu-H1-infected rats compared with control rats, indicating that Raf/MEK/ERK signaling was activated.

CONCLUSION

The data suggested that infection of neonatal rats with BDV Hu-H1 and Strain V caused behavioral abnormalities that shared common molecular pathways, providing preliminary evidences to investigate the underlying mechanisms of psychiatric disorders caused by BDV.

Identification of suitable reference genes for BDV-infected primary rat hippocampal neurons

Borna disease virus (BDV) is a neurotropic RNA virus that infects the limbic system of mammals and results in behavioral disorders. The hippocampus is a core region in the limbic system, which contributes to memory and learning and is important in the regulation of emotion. However, no validated microRNA housekeeping genes have yet been identified in BDV‑infected rat primary hippocampal neurons. Proper normalization is key in accurate miRNA expression analysis. The present study used reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) to evaluate the expression stability of 10 commonly used reference genes [miR‑92a, 5S, U6, miR‑103, miR‑101a, miR-let-7a, miR‑16, E2 small nucleolar RNA (snoRNA), U87 and miR‑191] in BDV‑infected rat hippocampal neurons and non‑infected controls across 12 days post‑infection. The data was analyzed by four statistical algorithms: geNorm, NormFinder, BestKeeper, and the comparative Δ‑Ct method. Subsequently, the most suitable reference genes (miR‑101a and U87) and the least suitable (snoRNA) were determined by the RankAggreg package. miR‑155 was selected as a standard by which to evaluate the most and least suitable reference genes. When normalized to the most stable reference gene there were significant differences between the two groups. However, when the data were normalized to the less stably expressed gene, the results were not significant. miR‑101a was recommended as a suitable reference gene for BDV-infected rat primary hippocampal neurons.

Identification and bioinformatic analysis of dysregulated microRNAs in human oligodendroglial cells infected with borna disease virus

MicroRNAs (miRNAs) are recognized as important regulators of gene expression via translational depression or mRNA degradation. Previously, dysregulated miRNAs have been found in neurodegenerative and neuropsychiatric disorders. Borna disease virus (BDV) is a neurotropic, negative single‑stranded RNA virus, which may be a cause of human neuropsychiatric disease. BDV is regarded as an ideal model to analyze the molecular mechanisms of mental disorders caused by viral infection. In the present study, 10 miRNAs were dysregulated in human oligodendrocytes (OL cells) infected with the BDV strain, Hu‑H1 (OL/BDV). The predicted target genes of those different miRNAs were closely associated with DNA binding, receptor activity, cytoplasm and membrane, biopolymer metabolic process and signal transduction, which were ranked highest using Gene Ontology (GO) analysis, and were predominantly involved in 'Immune system and adaptive Immune system pathways' on pathway analysis. Reverse transcription‑quantitative polymerase chain reaction analysis confirmed that seven miRNAs (miR‑1290, miR‑1908, miR‑146a‑5p, miR‑424‑5p, miR‑3676‑3p, miR‑296‑3p and miR‑7‑5p) were significantly downregulated in the OL/BDV cells, whereas two miRNAs (miR‑1244 and miR‑4521) showed no significant differences between the two groups. The present study revealed for the first time, to the best of our knowledge, the miRNA profile of BDV Hu‑H1‑infected human OL cells. Based on GO and pathway analyses, further investigation of the signaling processes in BDV‑infected oligodendrocytes may offer particular promise in improving understanding of the neuropathogenesis of BDV.

GC-MS-Based Metabonomic Profiling Displayed Differing Effects of Borna Disease Virus Natural Strain Hu-H1 and Laboratory Strain V Infection in Rat Cortical Neurons

Borna disease virus (BDV) persists in the central nervous systems of a wide variety of vertebrates and causes behavioral disorders. Previous studies have revealed that metabolic perturbations are associated with BDV infection. However, the pathophysiological effects of different viral strains remain largely unknown. Rat cortical neurons infected with human strain BDV Hu-H1, laboratory BDV Strain V, and non-infected control (CON) cells were cultured in vitro. At day 12 post-infection, a gas chromatography coupled with mass spectrometry (GC–MS) metabonomic approach was used to differentiate the metabonomic profiles of 35 independent intracellular samples from Hu-H1-infected cells (n = 12), Strain V-infected cells (n = 12), and CON cells (n = 11). Partial least squares discriminant analysis (PLS-DA) was performed to demonstrate discrimination between the three groups. Further statistical testing determined which individual metabolites displayed significant differences between groups. PLS-DA demonstrated that the whole metabolic pattern enabled statistical discrimination between groups. We identified 31 differential metabolites in the Hu-H1 and CON groups (21 decreased and 10 increased in Hu-H1 relative to CON), 35 differential metabolites in the Strain V and CON groups (30 decreased and 5 increased in Strain V relative to CON), and 21 differential metabolites in the Hu-H1 and Strain V groups (8 decreased and 13 increased in Hu-H1 relative to Strain V). Comparative metabonomic profiling revealed divergent perturbations in key energy and amino acid metabolites between natural strain Hu-H1 and laboratory Strain V of BDV. The two BDV strains differentially alter metabolic pathways of rat cortical neurons in vitro. Their systematic classification provides a valuable template for improved BDV strain definition in future studies.

Borna disease virus infection impacts microRNAs associated with nervous system development, cell differentiation, proliferation and apoptosis in the hippocampi of neonatal rats

MicroRNAs (miRNAs) regulate gene expression by inhibiting transcription or translation and are involved in diverse biological processes, including development, cellular differentiation and tumor generation. miRNA microarray technology is a high‑throughput global analysis tool for miRNA expression profiling. Here, the hippocampi of four borna disease virus (BDV)‑infected and four non‑infected control neonatal rats were selected for miRNA microarray and bioinformatic analysis. Reverse transcription quantitative polymerase chain reaction (RT‑qPCR) analysis was subsequently performed to validate the dysregulated miRNAs. Seven miRNAs (miR‑145*, miR‑146a*, miR‑192*, miR‑200b, miR‑223*, miR‑449a and miR‑505), showed increased expression, whereas two miRNAs (miR‑126 and miR‑374) showed decreased expression in the BDV‑infected group. By RT‑qPCR validation, five miRNAs (miR‑126, miR‑200b, miR‑374, miR‑449a and miR‑505) showed significantly decreased expression (P<0.05) in response to BDV infection. Biocarta pathway analysis predicted target genes associated with 'RNA', 'IGF1mTOR', 'EIF2', 'VEGF', 'EIF', 'NTHI', 'extrinsic', 'RB', 'IL1R' and 'IGF1' pathways. Gene Ontology analysis predicted target genes associated with 'peripheral nervous system development', 'regulation of small GTPase-mediated signal transduction', 'regulation of Ras protein signal transduction', 'aerobic respiration', 'membrane fusion', 'positive regulation of cell cycle', 'cellular respiration', 'heterocycle metabolic process', 'protein tetramerization' and 'regulation of Rho protein signal transduction' processes. Among the five dysregulated miRNAs identified by RT‑qPCR, miR‑126, miR‑200b and miR‑449a showed a strong association with nervous system development, cell differentiation, proliferation and apoptosis.

Decoding neuroproteomics: integrating the genome, translatome and functional anatomy

The immense intercellular and intracellular heterogeneity of the CNS presents major challenges for high-throughput omic analyses. Transcriptional, translational and post-translational regulatory events are localized to specific neuronal cell types or subcellular compartments, resulting in discrete patterns of protein expression and activity. A spatial and quantitative knowledge of the neuroproteome is therefore critical to understanding both normal and pathological aspects of the functional genomics and anatomy of the CNS. Improvements in mass spectrometry allow the profiling of proteins at a sufficient depth to complement results from high-throughput genomic and transcriptomic assays. However, there are challenges in integrating proteomic data with other data modalities and even greater challenges in obtaining comprehensive neuroproteomic data with cell-type specificity. Here we discuss how proteomics should be exploited to enhance high-throughput functional genomic analysis by tighter integration of data analyses. We also discuss experimental strategies to achieve finer cellular and subcellular resolution in transcriptomic and proteomic studies of neural tissues.

Human borna disease virus infection impacts host proteome and histone lysine acetylation in human oligodendroglia cells

Background

Borna disease virus (BDV) replicates in the nucleus and establishes persistent infections in mammalian hosts. A human BDV strain was used to address the first time, how BDV infection impacts the proteome and histone lysine acetylation (Kac) of human oligodendroglial (OL) cells, thus allowing a better understanding of infection-driven pathophysiology in vitro.

Methods

Proteome and histone lysine acetylation were profiled through stable isotope labeling for cell culture (SILAC)-based quantitative proteomics. The quantifiable proteome was annotated using bioinformatics. Histone acetylation changes were validated by biochemistry assays.

Results

Post BDV infection, 4383 quantifiable differential proteins were identified and functionally annotated to metabolism pathways, immune response, DNA replication, DNA repair, and transcriptional regulation. Sixteen of the thirty identified Kac sites in core histones presented altered acetylation levels post infection.

Conclusions

BDV infection using a human strain impacted the whole proteome and histone lysine acetylation in OL cells.

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A human strain of BDV (BDV Hu-H1) was used to infect human oligodendroglial cells (OL cells).

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This study is the first to reveal the host proteomic and histone Kac profiles in BDV-infected OL cells.

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BDV infection affected the expression of many transcription factors and several HATs and HDACs.