Proteomic analysis of the secretome of HepG2 cells indicates differential proteolytic processing after infection with dengue virus

Utility of Proteomics in Emerging and Re-Emerging Infectious Diseases Caused by RNA Viruses

Emerging and re-emerging infectious diseases due to RNA viruses cause major negative consequences for the quality of life, public health, and overall economic development. Most of the RNA viruses causing illnesses in humans are of zoonotic origin. Zoonotic viruses can directly be transferred from animals to humans through adaptation, followed by human-to-human transmission, such as in human immunodeficiency virus (HIV), severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and, more recently, SARS coronavirus 2 (SARS-CoV-2), or they can be transferred through insects or vectors, as in the case of Crimean-Congo hemorrhagic fever virus (CCHFV), Zika virus (ZIKV), and dengue virus (DENV). At the present, there are no vaccines or antiviral compounds against most of these viruses. Because proteins possess a vast array of functions in all known biological systems, proteomics-based strategies can provide important insights into the investigation of disease pathogenesis and the identification of promising antiviral drug targets during an epidemic or pandemic. Mass spectrometry technology has provided the capacity required for the precise identification and the sensitive and high-throughput analysis of proteins on a large scale and has contributed greatly to unravelling key protein-protein interactions, discovering signaling networks, and understanding disease mechanisms. In this Review, we present an account of quantitative proteomics and its application in some prominent recent examples of emerging and re-emerging RNA virus diseases like HIV-1, CCHFV, ZIKV, and DENV, with more detail with respect to coronaviruses (MERS-CoV and SARS-CoV) as well as the recent SARS-CoV-2 pandemic.

Proteomics of Select Neglected Tropical Diseases

Technological advances in mass spectrometry have enabled the extensive identification, characterization, and quantification of proteins in any biological system. In disease processes proteins are often altered in response to external stimuli; therefore, proteomics, the large-scale study of proteins and their functions, represents an invaluable tool for understanding the molecular basis of disease. This review highlights the use of mass spectrometry-based proteomics to study the pathogenesis, etiology, and pathology of several neglected tropical diseases (NTDs), a diverse group of disabling diseases primarily associated with poverty in tropical and subtropical regions of the world. While numerous NTDs have been the subject of proteomic studies, this review focuses on Buruli ulcer, dengue, leishmaniasis, and snakebite envenoming. The proteomic studies highlighted provide substantial information on the pathogenic mechanisms driving these diseases; they also identify molecular targets for drug discovery and development and uncover promising biomarkers that can assist in early diagnosis.

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis

We used a combination of experimental measurements and computer simulations to understand how liver cancer cells rewire their metabolism to grow faster. We observed that glutamate is excreted by the cells, and our simulations suggest that this occurs because glutamate is formed in excess in the cytoplasm, when cells rapidly synthesize nucleotides, which are required for growth. Meanwhile, glutamate that is formed in the mitochondria is, on the other hand, not excreted. Treating glutamate as two distinct pools, a cytosolic and a mitochondrial, is useful to better understand why many cancer cells rapidly consume glutamine, the precursor of glutamate. The results point toward potential drug targets that could be used to reduce growth of liver cancer cells.

Many cancer cells consume glutamine at high rates; counterintuitively, they simultaneously excrete glutamate, the first intermediate in glutamine metabolism. Glutamine consumption has been linked to replenishment of tricarboxylic acid cycle (TCA) intermediates and synthesis of adenosine triphosphate (ATP), but the reason for glutamate excretion is unclear. Here, we dynamically profile the uptake and excretion fluxes of a liver cancer cell line (HepG2) and use genome-scale metabolic modeling for in-depth analysis. We find that up to 30% of the glutamine is metabolized in the cytosol, primarily for nucleotide synthesis, producing cytosolic glutamate. We hypothesize that excreting glutamate helps the cell to increase the nucleotide synthesis rate to sustain growth. Indeed, we show experimentally that partial inhibition of glutamate excretion reduces cell growth. Our integrative approach thus links glutamine addiction to glutamate excretion in cancer and points toward potential drug targets.

In silico prediction of the secretome from the invasive neurotoxic marine dinoflagellate Alexandrium catenella

Alexandrium catenella, a marine dinoflagellate responsible for harmful algal blooms (HABs), proliferates with greater frequency, distribution and intensity, in disturbed marine coastal ecosystems. The proteins secreted into seawater may play a crucial role in maintaining this dinoflagellate in these ecosystems, but this possibility has never been investigated before. In this study, the A. catenella secretome was predicted from its transcriptome by combining several bioinformatics tools. Our results predict a secretome of 2 779 proteins, among which 79% contain less than 500 amino acids, suggesting that most secreted proteins are short in length. The predicted secretome includes 963 proteins (35%) with Pfam domains: 773 proteins with one Pfam domain and 190 proteins with two or more Pfam domains. Their functional annotation showed that they are mainly involved in (i) proteolysis, (ii) stress responses and (iii) primary metabolism. In addition, 47% of the secreted proteins appear to be enzymes, primarily peptidases, known to be biologically active in the extracellular medium during stress responses. Finally, this study provides a wealth of candidates of proteins secreted by A. catenella, which may interact with the marine environment and help this dinoflagellate develop in various environmental conditions.

Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses

To detect drug candidates for dengue haemorrhagic fever (DHF), we employed a computational drug repositioning method to perform an integrated multiple omics analysis based on transcriptomic, proteomic, and interactomic data. We identified 3,892 significant genes, 389 proteins, and 221 human proteins by transcriptomic analysis, proteomic analysis, and human–dengue virus protein–protein interactions, respectively. The drug candidates were selected using gene expression profiles for inverse drug–disease relationships compared with DHF patients and healthy controls as well as interactomic relationships between the signature proteins and chemical compounds. Integrating the results of the multiple omics analysis, we identified eight candidates for drug repositioning to treat DHF that targeted five proteins (ACTG1, CALR, ERC1, HSPA5, SYNE2) involved in human–dengue virus protein–protein interactions, and the signature proteins in the proteomic analysis mapped to significant pathways. Interestingly, five of these drug candidates, valparoic acid, sirolimus, resveratrol, vorinostat, and Y-27632, have been reported previously as effective treatments for flavivirus-induced diseases. The computational approach using multiple omics data for drug repositioning described in this study can be used effectively to identify novel drug candidates.

Proteomic analysis of A-549 cells infected with human adenovirus 40 by LC-MS

Human Adenoviruses (HAdVs) are etiological agents of different syndromes such as gastroenteritis, cystitis, ocular, and respiratory diseases, and infection by these viruses may cause alterations in cellular homeostasis. The objective of the study was the proteomic analysis of A-549 cells infected with HAdV-40 using LC-MS. At 30 h of infection, the quantitative analysis revealed 336 differentially expressed proteins. From them, 206 were induced (up-regulated) and 130 were suppressed (down-regulated). The majority of up-regulated proteins were related to energy, cellular organization, stress response, and apoptosis pathways. It was observed alteration of cell metabolism with increase of the glycolytic pathway, β-oxidation, and respiratory chain. Also, the results suggest cytoskeleton reorganization and apoptosis induction. The data can improve knowledge about the replication of HAdV-40 in cell culture considering the proteins related to distinct metabolic pathways induced by viral infection in A-549 cells.

Systems Biology Reveals NS4B-Cyclophilin A Interaction: A New Target to Inhibit YFV Replication

Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 proteins confirmed using Scaffold 3 Software. Cyclophilin A (CypA), a protein that has been shown to be necessary for the positive regulation of flavivirus replication, was identified as a possible NS4B partner. 59 proteins were found to be significantly increased when compared with a negative control, and CypA exhibited the greatest difference, with a 22-fold change. Fisher's exact test was significant for 58 proteins, and the p value of CypA was the most significant (0.000000019). The Ingenuity Systems software identified 16 pathways, and this analysis indicated sirolimus, an mTOR pathway inhibitor, as a potential inhibitor of CypA. Immunofluorescence and viral plaque assays showed a significant reduction in YFV replication using sirolimus and cyclosporine A (CsA) as inhibitors. Furthermore, YFV replication was strongly inhibited in cells treated with both inhibitors using reporter BHK-21-rep-YFV17D-LucNeoIres cells. Taken together, these data suggest that CypA-NS4B interaction regulates YFV replication. Finally, we present the first evidence that YFV inhibition may depend on NS4B-CypA interaction.