bims-mevinf 2024-06-30 papers

bims-mevinf

Biomed News

on Metabolism in viral infections

Issue of 2024–06–30
twelve papers selected by
Alexander Ivanov, Engelhardt Institute of Molecular Biology

Hepatitis C Virus Dysregulates Polyamine and Proline Metabolism and Perturbs the Urea Cycle.
ISKNV Triggers AMPK/mTOR-Mediated Autophagy Signaling through Oxidative Stress, Inducing Antioxidant Enzyme Expression and Enhancing Viral Replication in GF-1 Cells.
Dengue Virus Dependence on Glucokinase Activity and Glycolysis Confers Sensitivity to NAD(H) Biosynthesis Inhibitors.
Significance of Cellular Lipid Metabolism for the Replication of Rotaviruses and Other RNA Viruses.
Reactive Oxygen Species Induction by Hepatitis B Virus: Implications for Viral Replication in p53-Positive Human Hepatoma Cells.
Respiratory Virus-Induced PARP1 Alters DC Metabolism and Antiviral Immunity Inducing Pulmonary Immunopathology.
Virus infection and sphingolipid metabolism.
Essential functions of inositol hexakisphosphate (IP6) in murine leukemia virus replication.
The global role of G6PD in infection and immunity.
Verapamil inhibits respiratory syncytial virus infection by regulating Ca2+ influx.
Identification and Analysis of Biomarkers Associated with Lipophagy and Therapeutic Agents for COVID-19.
Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development.

Cells. 2024 Jun 14. pii: 1036. [Epub ahead of print]13(12):

Hepatitis C Virus Dysregulates Polyamine and Proline Metabolism and Perturbs the Urea Cycle.

Natalia F Zakirova, Olga A Khomich, Olga A Smirnova, Jennifer Molle, Sarah Duponchel, Dmitry V Yanvarev, Vladimir T Valuev-Elliston, Lea Monnier, Boyan Grigorov, Olga N Ivanova, Inna L Karpenko, Mikhail V Golikov, Cedric Bovet, Barbara Rindlisbacher, Alex R Khomutov, Sergey N Kochetkov, Birke Bartosch, Alexander V Ivanov.

  Hepatitis C virus (HCV) is an oncogenic virus that causes chronic liver disease in more than 80% of patients. During the last decade, efficient direct-acting antivirals were introduced into clinical practice. However, clearance of the virus does not reduce the risk of end-stage liver diseases to the level observed in patients who have never been infected. So, investigation of HCV pathogenesis is still warranted. Virus-induced changes in cell metabolism contribute to the development of HCV-associated liver pathologies. Here, we studied the impact of the virus on the metabolism of polyamines and proline as well as on the urea cycle, which plays a crucial role in liver function. It was found that HCV strongly suppresses the expression of arginase, a key enzyme of the urea cycle, leading to the accumulation of arginine, and up-regulates proline oxidase with a concomitant decrease in proline concentrations. The addition of exogenous proline moderately suppressed viral replication. HCV up-regulated transcription but suppressed protein levels of polyamine-metabolizing enzymes. This resulted in a decrease in polyamine content in infected cells. Finally, compounds targeting polyamine metabolism demonstrated pronounced antiviral activity, pointing to spermine and spermidine as compounds affecting HCV replication. These data expand our understanding of HCV's imprint on cell metabolism.

Keywords:  antiviral agents; hepatitis C virus; polyamines; proline metabolism; urea cycle

DOI:  https://doi.org/10.3390/cells13121036
Viruses. 2024 Jun 04. pii: 914. [Epub ahead of print]16(6):

ISKNV Triggers AMPK/mTOR-Mediated Autophagy Signaling through Oxidative Stress, Inducing Antioxidant Enzyme Expression and Enhancing Viral Replication in GF-1 Cells.

Tsai-Ching Hsueh, Pin-Han Chen, Jiann-Ruey Hong.

  Infectious spleen and kidney necrosis virus (ISKNV) infections can induce the process of host cellular autophagy but have rarely been identified within the molecular autophagy signaling pathway. In the present study, we demonstrated that ISKNV induces ROS-mediated oxidative stress signals for the induction of 5'AMP-activated protein kinase/mechanistic target of rapamycin kinase (AMPK/mTOR)-mediated autophagy and upregulation of host antioxidant enzymes in fish GF-1 cells. We also examined ISKNV-induced oxidative stress, finding that reactive oxidative species (ROS) increased by 1.5-fold and 2.5-fold from day 2 to day 3, respectively, as assessed by the H2DCFDA assay for tracing hydrogen peroxide (H2O2), which was blocked by NAC treatment in fish GF-1 cells. Furthermore, ISKNV infection was shown to trigger oxidative stress/Nrf2 signaling from day 1 to day 3; this event was then correlated with the upregulation of antioxidant enzymes such as Cu/ZnSOD and MnSOD and was blocked by the antioxidant NAC. Using an MDC assay, TEM analysis and autophagy marker LC3-II/I ratio, we found that ROS stress can regulate autophagosome formation within the induction of autophagy, which was inhibited by NAC treatment in GF-1 cells. Through signal analysis, we found that AMPK/mTOR flux was modulated through inhibition of mTOR and activation of AMPK, indicating phosphorylation levels of mTOR Ser 2448 and AMPK Thr 172 from day 1 to day 3; however, this process was reversed by NAC treatment, which also caused a reduction in virus titer (TCID50%) of up to 1000 times by day 3 in GF-1 cells. Thus, ISKNV-induced oxidative stress signaling is blocked by antioxidant NAC, which can also either suppress mTOR/AMPK autophagic signals or reduce viral replication. These findings may provide the basis for the creation of DNA control and treatment strategies.

Keywords:  DNA virus; ISKNV; ROS; antioxidant NAC; autophagy; fish; mTOR; oxidative stress

DOI:  https://doi.org/10.3390/v16060914
Antiviral Res. 2024 Jun 21. pii: S0166-3542(24)00148-7. [Epub ahead of print] 105939

Dengue Virus Dependence on Glucokinase Activity and Glycolysis Confers Sensitivity to NAD(H) Biosynthesis Inhibitors.

Eva Ogire, Laure Perrin-Cocon, Marianne Figl, Cindy Kundlacz, Clémence Jacquemin, Sophie Hubert, Anne Aublin-Gex, Johan Toesca, Christophe Ramière, Pierre-Olivier Vidalain, Cyrille Mathieu, Vincent Lotteau, Olivier Diaz.

  Viruses have developed sophisticated strategies to control metabolic activity of infected cells in order to supply replication machinery with energy and metabolites. Dengue virus (DENV), a mosquito-borne flavivirus responsible for dengue fever, is no exception. Previous reports have documented DENV interactions with metabolic pathways and shown in particular that glycolysis is increased in DENV-infected cells. However, underlying molecular mechanisms are still poorly characterized and dependence of DENV on this pathway has not been investigated in details yet. Here, we identified an interaction between the non-structural protein 3 (NS3) of DENV and glucokinase regulator protein (GCKR), a host protein that inhibits the liver-specific hexokinase GCK. NS3 expression was found to increase glucose consumption and lactate secretion in hepatic cell line expressing GCK. Interestingly, we observed that GCKR interaction with GCK decreases DENV replication, indicating the dependence of DENV to GCK activity and supporting the role of NS3 as an inhibitor of GCKR function. Accordingly, in the same cells, DENV replication both induces and depends on glycolysis. By targeting NAD(H) biosynthesis with the antimetabolite 6-Amino-Nicotinamide (6-AN), we decreased cellular glycolytic activity and inhibited DENV replication in hepatic cells. Infection of primary organotypic liver cultures (OLiC) from hamsters was also inhibited by 6-AN. Altogether, our results show that DENV has evolved strategies to control glycolysis in the liver, which could account for hepatic dysfunctions associated to infection. Besides, our findings suggest that lowering intracellular availability of NAD(H) could be a valuable therapeutic strategy to control glycolysis and inhibit DENV replication in the liver.

Keywords:  Dengue Virus NS3; NAD(H) metabolism; glucokinase regulator protein; glycolysis; hepatocyte; primary organotypic liver cultures

DOI:  https://doi.org/10.1016/j.antiviral.2024.105939
Viruses. 2024 Jun 04. pii: 908. [Epub ahead of print]16(6):

Significance of Cellular Lipid Metabolism for the Replication of Rotaviruses and Other RNA Viruses.

Ulrich Desselberger.

  The replication of species A rotaviruses (RVAs) involves the recruitment of and interaction with cellular organelles' lipid droplets (LDs), both physically and functionally. The inhibition of enzymes involved in the cellular fatty acid biosynthesis pathway or the inhibition of cellular lipases that degrade LDs was found to reduce the functions of 'viral factories' (viroplasms for rotaviruses or replication compartments of other RNA viruses) and decrease the production of infectious progeny viruses. While many other RNA viruses utilize cellular lipids for their replication, their detailed analysis is far beyond this review; only a few annotations are made relating to hepatitis C virus (HCV), enteroviruses, SARS-CoV-2, and HIV-1.

Keywords:  HIV-1; RNA virus replication; SARS-CoV-2; enteroviruses; hepatitis C virus; lipid metabolism; rotavirus

DOI:  https://doi.org/10.3390/v16060908
Int J Mol Sci. 2024 Jun 15. pii: 6606. [Epub ahead of print]25(12):

Reactive Oxygen Species Induction by Hepatitis B Virus: Implications for Viral Replication in p53-Positive Human Hepatoma Cells.

Yuna Jeong, Jiwoo Han, Kyung Lib Jang.

  Hepatitis B virus (HBV) infects approximately 300 million people worldwide, causing chronic infections. The HBV X protein (HBx) is crucial for viral replication and induces reactive oxygen species (ROS), leading to cellular damage. This study explores the relationship between HBx-induced ROS, p53 activation, and HBV replication. Using HepG2 and Hep3B cell lines that express the HBV receptor NTCP, we compared ROS generation and HBV replication relative to p53 status. Results indicated that HBV infection significantly increased ROS levels in p53-positive HepG2-NTCP cells compared to p53-deficient Hep3B-NTCP cells. Knockdown of p53 reduced ROS levels and enhanced HBV replication in HepG2-NTCP cells, whereas p53 overexpression increased ROS and inhibited HBV replication in Hep3B-NTCP cells. The ROS scavenger N-acetyl-L-cysteine (NAC) reversed these effects. The study also found that ROS-induced degradation of the HBx is mediated by the E3 ligase Siah-1, which is activated by p53. Mutations in p53 or inhibition of its transcriptional activity prevented ROS-mediated HBx degradation and HBV inhibition. These findings reveal a p53-dependent negative feedback loop where HBx-induced ROS increases p53 levels, leading to Siah-1-mediated HBx degradation and HBV replication inhibition. This study offers insights into the molecular mechanisms of HBV replication and identifies potential therapeutic targets involving ROS and p53 pathways.

Keywords:  HBx; Hepatitis B virus; Siah-1; p53; proteasome; reactive oxygen species

DOI:  https://doi.org/10.3390/ijms25126606
Viruses. 2024 Jun 04. pii: 910. [Epub ahead of print]16(6):

Respiratory Virus-Induced PARP1 Alters DC Metabolism and Antiviral Immunity Inducing Pulmonary Immunopathology.

Mohamed M Mire, Srikanth Elesela, Susan Morris, Gabriel Corfas, Andrew Rasky, Nicholas W Lukacs.

  Previous studies from our laboratory and others have established the dendritic cell (DC) as a key target of RSV that drives infection-induced pathology. Analysis of RSV-induced transcriptomic changes in RSV-infected DC revealed metabolic gene signatures suggestive of altered cellular metabolism. Reverse phase protein array (RPPA) data showed significantly increased PARP1 phosphorylation in RSV-infected DC. Real-time cell metabolic analysis demonstrated increased glycolysis in PARP1-/- DC after RSV infection, confirming a role for PARP1 in regulating DC metabolism. Our data show that enzymatic inhibition or genomic ablation of PARP1 resulted in increased ifnb1, il12, and il27 in RSV-infected DC which, together, promote a more appropriate anti-viral environment. PARP1-/- mice and PARP1-inhibitor-treated mice were protected against RSV-induced immunopathology including airway inflammation, Th2 cytokine production, and mucus hypersecretion. However, delayed treatment with PARP1 inhibitor in RSV-infected mice provided only partial protection, suggesting that PARP1 is most important during the earlier innate immune stage of RSV infection.

Keywords:  cell metabolism; dendritic cell; innate immunity; virus infection

DOI:  https://doi.org/10.3390/v16060910
Antiviral Res. 2024 Jun 21. pii: S0166-3542(24)00151-7. [Epub ahead of print]228 105942

Virus infection and sphingolipid metabolism.

Jun Dai, Yiyi Feng, Ying Liao, Lei Tan, Yingjie Sun, Cuiping Song, Xusheng Qiu, Chan Ding.

  Cellular sphingolipids have vital roles in human virus replication and spread as they are exploited by viruses for cell entry, membrane fusion, genome replication, assembly, budding, and propagation. Intracellular sphingolipid biosynthesis triggers conformational changes in viral receptors and facilitates endosomal escape. However, our current understanding of how sphingolipids precisely regulate viral replication is limited, and further research is required to comprehensively understand the relationships between viral replication and endogenous sphingolipid species. Emerging evidence now suggests that targeting and manipulating sphingolipid metabolism enzymes in host cells is a promising strategy to effectively combat viral infections. Additionally, serum sphingolipid species and concentrations could function as potential serum biomarkers to help monitor viral infection status in different patients. In this work, we comprehensively review the literature to clarify how viruses exploit host sphingolipid metabolism to accommodate viral replication and disrupt host innate immune responses. We also provide valuable insights on the development and use of antiviral drugs in this area.

Keywords:  Endosomal escape; Serum biomarker; Sphingolipid; Sphingolipid rheostat; Virus

DOI:  https://doi.org/10.1016/j.antiviral.2024.105942
mBio. 2024 Jun 24. e0115824

Essential functions of inositol hexakisphosphate (IP6) in murine leukemia virus replication.

Banhi Biswas, Kin Kui Lai, Harrison Bracey, Siddhartha A K Datta, Demetria Harvin, Gregory A Sowd, Christopher Aiken, Alan Rein.

  We have investigated the function of inositol hexakisphosphate (IP6) and inositol pentakisphosphate (IP5) in the replication of murine leukemia virus (MLV). While IP6 is known to be critical for the life cycle of HIV-1, its significance in MLV remains unexplored. We find that IP6 is indeed important for MLV replication. It significantly enhances endogenous reverse transcription (ERT) in MLV. Additionally, a pelleting-based assay reveals that IP6 can stabilize MLV cores, thereby facilitating ERT. We find that IP5 and IP6 are packaged in MLV particles. However, unlike HIV-1, MLV depends upon the presence of IP6 and IP5 in target cells for successful infection. This IP6/5 requirement for infection is reflected in impaired reverse transcription observed in IP6/5-deficient cell lines. In summary, our findings demonstrate the importance of capsid stabilization by IP6/5 in the replication of diverse retroviruses; we suggest possible reasons for the differences from HIV-1 that we observed in MLV.IMPORTANCEInositol hexakisphosphate (IP6) is crucial for the assembly and replication of HIV-1. IP6 is packaged in HIV-1 particles and stabilizes the viral core enabling it to synthesize viral DNA early in viral infection. While its importance for HIV-1 is well established, its significance for other retroviruses is unknown. Here we report the role of IP6 in the gammaretrovirus, murine leukemia virus (MLV). We found that like HIV-1, MLV packages IP6, and as in HIV-1, IP6 stabilizes the MLV core thus promoting reverse transcription. Interestingly, we discovered a key difference in the role of IP6 in MLV versus HIV-1: while HIV-1 is not dependent upon IP6 levels in target cells, MLV replication is significantly reduced in IP6-deficient cell lines. We suggest that this difference in IP6 requirements reflects key differences between HIV-1 and MLV replication.

Keywords:  IP6; inositol hexakisphosphate; murine leukemia virus; retroviruses; virus structure

DOI:  https://doi.org/10.1128/mbio.01158-24
Front Immunol. 2024 ;15 1393213

The global role of G6PD in infection and immunity.

Shivang S Shah, Elizabeth F Stone, Richard O Francis, Matthew S Karafin.

  Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzymopathy in humans. G6PD is an essential enzyme in the pentose phosphate pathway (PPP), generating NADPH needed for cellular biosynthesis and reactive oxygen species (ROS) homeostasis, the latter especially key in red blood cells (RBCs). Beyond the RBC, there is emerging evidence that G6PD exerts an immunologic role by virtue of its functions in leukocyte oxidative metabolism and anabolic synthesis necessary for immune effector function. We review these here, and consider the global immunometabolic role of G6PD activity and G6PD deficiency in modulating inflammation and immunopathology.

Keywords:  G6PD; G6PD deficiency; glucose-6-phosphate dehydrogenase; immunity; immunometabolism

DOI:  https://doi.org/10.3389/fimmu.2024.1393213
Life Sci. 2024 Jun 26. pii: S0024-3205(24)00467-3. [Epub ahead of print] 122877

Verapamil inhibits respiratory syncytial virus infection by regulating Ca2+ influx.

Fang Chen, Huyan Shen, Gang Liu, Pingping Zhang, Lin Zhang, Siyu Lin, Han Gao, Hong Peng, Yan-Fei Qi, Yan Chen, Yinhui Jiang, Jiandong Huang, Xiangchun Shen, Yu-Si Luo, Ke Zhang.

   AIMS: The study evaluated the antiviral effect of Verapamil against respiratory syncytial virus (RSV) and investigated its underlying mechanism.
MATERIALS AND METHODS: RSV-infected BALB/c mice were treated with Verapamil. Body weight, survival rates, viral load, lung damage, inflammatory factors, and the expression of RSV fusion (F) protein were analyzed. In cellular studies, intracellular Ca2+ and viral titers were measured in the presence of Verapamil, Calcium Chloride, and EGTA. A time-of-addition assay assessed the antiviral effect of Verapamil.
KEY FINDINGS: Mice infected with RSV and treated with Verapamil exhibited a significant decrease in weight loss, an increase in survival rates, and reductions in viral titers, RSV F protein expression, inflammatory responses, and lung tissue injury. Verapamil reduced intracellular calcium levels, which correlated with reduced viral titers. The addition of calcium chloride reversed the anti-viral effects mediated by Verapamil, while EGTA potentiated them. The antiviral activity of Verapamil was observed during the early phase of RSV infection, likely by blocking Ca2+ channels and inhibiting virus replication.
SIGNIFICANCE: Verapamil effectively inhibits RSV infection by blocking calcium channels and reducing intracellular calcium levels, thereby impeding viral replication. Thus, Verapamil shows promise as a treatment for RSV.

Keywords:  Anti-virus; Ca(2+); EGTA; Respiratory syncytial virus; Verapamil

DOI:  https://doi.org/10.1016/j.lfs.2024.122877
Viruses. 2024 Jun 07. pii: 923. [Epub ahead of print]16(6):

Identification and Analysis of Biomarkers Associated with Lipophagy and Therapeutic Agents for COVID-19.

Yujia Wu, Zhenlin Wu, Qiying Jin, Jinyuan Liu, Peiping Xu.

   BACKGROUND: Lipids, as a fundamental cell component, play an regulating role in controlling the different cellular biological processes involved in viral infections. A notable feature of coronavirus disease 2019 (COVID-19) is impaired lipid metabolism. The function of lipophagy-related genes in COVID-19 is unknown. The present study aimed to investigate biomarkers and drug targets associated with lipophagy and lipophagy-based therapeutic agents for COVID-19 through bioinformatics analysis.
METHODS: Lipophagy-related biomarkers for COVID-19 were identified using machine learning algorithms such as random forest, Support Vector Machine-Recursive Feature Elimination, Generalized Linear Model, and Extreme Gradient Boosting in three COVID-19-associated GEO datasets: scRNA-seq (GSE145926) and bulk RNA-seq (GSE183533 and GSE190496). The cMAP database was searched for potential COVID-19 medications.
RESULTS: The lipophagy pathway was downregulated, and the lipid droplet formation pathway was upregulated, resulting in impaired lipid metabolism. Seven lipophagy-related genes, including ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2, were used as biomarkers and drug targets for COVID-19. Moreover, lipophagy may play a role in COVID-19 pathogenesis. As prospective drugs for treating COVID-19, seven potential downregulators (phenoxybenzamine, helveticoside, lanatoside C, geldanamycin, loperamide, pioglitazone, and trichostatin A) were discovered. These medication candidates showed remarkable binding energies against the seven biomarkers.
CONCLUSIONS: The lipophagy-related genes ACADVL, HYOU1, DAP, AUP1, PRXAB2, LSS, and PLIN2 can be used as biomarkers and drug targets for COVID-19. Seven potential downregulators of these seven biomarkers may have therapeutic effects for treating COVID-19.

Keywords:  COVID-19; bioinformatics; lipid metabolism; lipophagy-related genes; therapeutic agents

DOI:  https://doi.org/10.3390/v16060923
Poult Sci. 2024 Jun 14. pii: S0032-5791(24)00558-3. [Epub ahead of print]103(9): 103979

Single-nucleus transcriptome reveals cell dynamic response of liver during the late chick embryonic development.

Huimei Wang, Jiongyan Liu, Pinhui Zhu, Lin Shi, Yanli Liu, Xiaojun Yang, Xin Yang.

  The late embryonic development of the liver, a major metabolic organ, remains poorly characterized at single cell resolution. Here, we used single-nucleus RNA-sequencing (snRNA-seq) to characterize the chicken liver cells at 2 embryonic development time points (E14 and D1). We uncovered 8 cell types including hepatocytes, endothelial cells, hepatic stellate cells, erythrocytes, cholangiocytes, kupffer cells, mesothelial cells, and lymphocytes. And we discovered significant differences in the abundance of different cell types between E14 and D1. Moreover, we characterized the heterogeneity of hepatocytes, endothelial cells, and mesenchymal cells based on the gene regulatory networks of each clusters. Trajectory analyses revealed 128 genes associated with hepatocyte development and function, including apolipoprotein genes involved hepatic lipid metabolism and NADH dehydrogenase subunits involved hepatic oxidative phosphorylation. Furthermore, we identified the differentially expressed genes (DEGs) between E14 and D1 at the cellular levels, which contribute to changes in liver development and function. These DEGs were significantly enriched in PPAR signaling pathways and lipid metabolism related pathways. Our results presented the single-cell mapping of chick embryonic liver at late stages of development and demonstrated the metabolic changes across the 2 age stages at the cellular level, which can help to further study the molecular development mechanism of embryonic liver.

Keywords:  chicken; embryo; liver; single-nucleus RNA-seq

DOI:  https://doi.org/10.1016/j.psj.2024.103979