Interactome networks between the human respiratory syncytial virus (HRSV), the human metapneumovirus (ΗMPV), and their host: In silico investigation and comparative functional enrichment analysis

Human Peripheral Blood Leukocyte Transcriptome-Based Aging Clock Reveals Acceleration of Aging by Bacterial or Viral Infections

The aging of the population is a global concern. In the post-coronavirus disease 2019 (COVID-19) pandemic era, there are no effective methods to identify aging acceleration due to infection. In this study, we conducted whole-transcriptome sequencing on peripheral blood samples from 35 healthy individuals (22-88 years old). By analyzing the changes in mRNA, lncRNA, and miRNA expression, we investigated the characteristics of transcriptome alterations during the aging process. ceRNA networks were constructed, and 10 genes (CD248, PHGDH, SFXN2, MXRA8, NOG, TTC24, PHYKPL, CACHD1, BPGM, and TWF1) were identified as potential aging markers and used to construct an aging clock. Moreover, our aging clock categorized individuals into slow-, average-, and quick-aging groups, highlighting a link between accelerated aging and infection-related clinical parameters. Pseudotime analysis further revealed 2 distinct aging trajectories, corroborating the variations in the aging rate identified by the aging clock. Furthermore, we validated the results using the OEP001041 data set (277 healthy individuals aged 17-75), and data sets comprising patients with infectious diseases (n = 1 558). Our study revealed that infection accelerates aging via increased inflammation and oxidative stress in infectious disease patients. Besides, the aging clock exhibited alterations after infection, highlighting its potential for assessing the aging rate after patient recovery. In conclusion, our study introduces a novel aging clock to assess the aging rate in healthy individuals and those with infections, revealing a strong link between accelerated aging and infections through inflammation and oxidative stress. These findings offer valuable insights into aging mechanisms and potential strategies for healthy aging.

The Neglected Suppressor of Cytokine Signalling (SOCS): SOCS4-7

SOCS proteins are essential for the regulation of oncogenic, anti-pathogenic, and proinflammatory signalling cascades, including the JAK/STAT and NF-kB pathways, where they act as negative feedback regulators. Given their powerful role in a broad spectrum of biological processes, it is surprising that the functions of many SOCS proteins have not been widely explored. While the mechanisms of action of CIS, SOCS1-3 are well-documented, information regarding SOCS4-7 remains limited. However, recent studies have begun to elucidate the regulatory functions of these proteins during infection and disease, such as influenza infection, cancer and diabetes. Therefore, this review aims to describe and discuss studies detailing our current understanding of SOCS4-7, painting a clearer picture of the biological processes these regulatory proteins maintain. Indeed, our review highlights important evidence proving that all SOCS play a role in biological processes that are essential for normal immunological homeostasis, clearance of infection and avoidance of disease. Understanding how SOCS proteins interact with other proteins or how they are dysregulated in disease is likely to provide valuable insights for advancing therapeutic approaches.

Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research

Computer-aided analysis of proteins or nucleic acids seems like a matter of course nowadays; however, the history of Bioinformatics and Computational Biology is quite recent. The advent of high-throughput sequencing has led to the production of "big data", which has also affected the field of virology. The collaboration between the communities of bioinformaticians and virologists already started a few decades ago and it was strongly enhanced by the recent SARS-CoV-2 pandemics. In this article, which is the first in a series on how bioinformatics can enhance virus research, we show that highly useful information is retrievable from selected general and dedicated databases. Indeed, an enormous amount of information-both in terms of nucleotide/protein sequences and their annotation-is deposited in the general databases of international organisations participating in the International Nucleotide Sequence Database Collaboration (INSDC). However, more and more virus-specific databases have been established and are progressively enriched with the contents and features reported in this article. Since viruses are intracellular obligate parasites, a special focus is given to host-pathogen protein-protein interaction databases. Finally, we illustrate several phylogenetic and phylodynamic tools, combining information on algorithms and features with practical information on how to use them and case studies that validate their usefulness. Databases and tools for functional inference will be covered in the next article of this series: Bioinformatics goes viral: II. Sequence-based and structure-based functional analyses for boosting virus research.

Network pharmacology analysis of Chandraprabha Vati: A new hope for the treatment of Metabolic Syndrome

BACKGROUND

Drug research is increasingly using Network Pharmacology (NP) to tackle complex conditions like Metabolic Syndrome (MetS), which is characterized by obesity, hyperglycemia, and dyslipidemia. Single-action drugs are inadequate to treat MetS, which is marked by a range of complications including glucose intolerance, hyperlipidemia, mitochondrial dysfunction, and inflammation.

OBJECTIVES

To analyze Chandraprabha vati using Network Pharmacology to assess its potential in alleviating MetS-related complications.

MATERIAL AND METHODS

The genes related to MetS, inflammation, and the target genes of the CPV components were identified using network pharmacology tools like DisgNET and BindingDB. Followed by mapping of the CPV target genes with the genes implicated in MetS and inflammation to identify putative potential targets. Gene ontology, pathway enrichment analysis, and STRING database were employed for further exploration. Furthermore, drug-target-protein interactions network were visualized using Cytoscape 3.9.1.

RESULTS

The results showed that out of the 225 target genes of the CPV components, 33 overlapping and 19 non-overlapping genes could be potential targets for MetS. Similarly, 14 overlapping and 7 non-overlapping genes could be potential targets for inflammation. The CPV bioactives target genes were found to be involved in lipid and insulin homeostasis via several pathways revealed by the pathway analysis. The importance of CPV in treating MetS was supported by GO enrichment data; this could be due to its potential to influence pathways linked to metabolism, ER stress, mitochondrial dysfunction, oxidative stress, and inflammation.

CONCLUSIONS

These results offer a promising approach to developing treatment and repurposing CPV for complex conditions such as MetS.

In silico comparative structural and compositional analysis of glycoproteins of RSV to study the nature of stability and transmissibility of RSV A

The current scenario of COVID-19 makes us to think about the devastating diseases that kill so many people every year. Analysis of viral proteins contributes many things that are utterly useful in the evolution of therapeutic drugs and vaccines. In this study, sequence and structure of fusion glycoproteins and major surface glycoproteins of respiratory syncytial virus (RSV) were analysed to reveal the stability and transmission rate. RSV A has the highest abundance of aromatic residues. The Kyte-Doolittle scale indicates the hydrophilic nature of RSV A protein which leads to the higher transmission rate of this virus. Intra-protein interactions such as carbonyl interactions, cation-pi, and salt bridges were shown to be greater in RSV A compared to RSV B, which might lead to improved stability. This study discovered the presence of a network aromatic-sulphur interaction in viral proteins. Analysis of ligand binding pocket of RSV proteins indicated that drugs are performing better on RSV B than RSV A. It was also shown that increasing the number of tunnels in RSV A proteins boosts catalytic activity. This study will be helpful in drug discovery and vaccine development.

A New Prospect for the Treatment of Nephrotic Syndrome Based on Network Pharmacology Analysis

Network pharmacology is an emerging field which is currently capturing interest in drug discovery and development. Chronic kidney conditions have become a threat globally due to its associated lifelong therapies. Nephrotic syndrome (NS) is a common glomerular disease that is seen in paediatric and adult population with characteristic manifestation of proteinuria, oedema, hypoalbuminemia, and hyperlipidemia. It involves podocyte damage with tubulointerstitial fibrosis and glomerulosclerosis. Till date there has been no specific treatment available for this condition that provides complete remission. Repurposing of drugs can thus be a potential strategy for the treatment of NS. Recently, epigenetic mechanisms were identified that promote progression of many renal diseases. Therefore, in the present study, we investigated two epigenetic drugs valproic acid (VPA) and all-trans retinoic acid (ATRA). Epigenetic drugs act by binging about changes in gene expression without altering the DNA sequence. The changes include DNA methylation or histone modifications. The targets for the two drugs ATRA and VPA were collated from ChEMBL and Binding DB. All the genes associated with NS were collected from DisGeNET and KEGG database. Interacting proteins for the target genes were acquired from STRING database. The genes were then subjected to gene ontology and pathway enrichment analysis using a functional enrichment software tool. A drug-target and drug-potential target-protein interaction network was constructed using the Cytoscape software. Our results revealed that the two drugs VPA and ATRA had 65 common targets that contributed to kidney diseases. Out of which, 25 targets were specifically NS associated. Further, our work exhibited that ATRA and VPA were synergistically involved in pathways of inflammation, renal fibrosis, glomerulosclerosis and possibly mitochondrial biogenesis and endoplasmic reticulum stress. We thus propose a synergistic potential of the two drugs for treating chronic kidney diseases, specifically NS. The outcomes will undoubtedly invigorate further preclinical and clinical explorative studies. We identify network pharmacology as an initial inherent approach in identifying drug candidates for repurposing and synergism.

Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV) is the main cause of acute respiratory infections in young children and also has a major impact on the elderly and immunocompromised people. In the absence of a vaccine or efficient treatment, a better understanding of RSV interactions with the host antiviral response during infection is needed. Previous studies revealed that cytoplasmic inclusion bodies (IBs), where viral replication and transcription occur, could play a major role in the control of innate immunity during infection by recruiting cellular proteins involved in the host antiviral response. We recently showed that the morphogenesis of IBs relies on a liquid-liquid-phase separation mechanism depending on the interaction between viral nucleoprotein (N) and phosphoprotein (P). These scaffold proteins are expected to play a central role in the recruitment of cellular proteins to IBs. Here, we performed a yeast two-hybrid screen using RSV N protein as bait and identified the cellular protein TAX1BP1 as a potential partner of this viral protein. This interaction was validated by pulldown and immunoprecipitation assays. We showed that TAX1BP1 suppression has only a limited impact on RSV infection in cell cultures. However, RSV replication is decreased in TAX1BP1-deficient (TAX1BP1 knockout [TAX1BP1KO]) mice, whereas the production of inflammatory and antiviral cytokines is enhanced. In vitro infection of wild-type or TAX1BP1KO alveolar macrophages confirmed that the innate immune response to RSV infection is enhanced in the absence of TAX1BP1. Altogether, our results suggest that RSV could hijack TAX1BP1 to restrain the host immune response during infection. IMPORTANCE Respiratory syncytial virus (RSV), which is the leading cause of lower respiratory tract illness in infants, remains a medical problem in the absence of a vaccine or efficient treatment. This virus is also recognized as a main pathogen in the elderly and immunocompromised people, and the occurrence of coinfections (with other respiratory viruses and bacteria) amplifies the risks of developing respiratory distress. In this context, a better understanding of the pathogenesis associated with viral respiratory infections, which depends on both viral replication and the host immune response, is needed. The present study reveals that the cellular protein TAX1BP1, which interacts with the RSV nucleoprotein N, participates in the control of the innate immune response during RSV infection, suggesting that the N-TAX1BP1 interaction represents a new target for the development of antivirals.