Proteomics for Uncovering the Pathologies of Emerging Viruses

By Elene Tsopurashvili (elenet@princeton.edu) and Katelyn C. Cook (katelync@princeton.edu)

June 23, 2020

 

The identification and study of “emerging” viruses is a critical focus of biomedical research. An emerging human virus is a pathogen that meets the following criteria: 1) A virus that recently entered the human population, and/or 2) A virus that already infects humans at low frequency but recently increased in transmission rate or has the potential to do so. This is driven by a combination of ecological and socioeconomical factors, especially those that result in increased or variable crosstalk between humans and animals. For example, human immunodeficiency virus (HIV, 1959-present), Ebola virus (EBV, 1976-present), swine flu (H1N1/09 influenza, 2009), and Middle East respiratory syndrome-related coronavirus (MERS-CoV, 2012-present), among others, are emerging viruses that arose via novel transmission from animal reservoirs: chimpanzees, bats, pigs, and camels/bats, respectively.

In contrast to viruses widely circulating within the human population – such as herpesviruses, which have co-evolved with their hosts since the evolution of mammals – the pathologies of emerging viruses are usually uncharacterized, posing a significant barrier for the development of vaccines and antiviral therapeutics. Exacerbating this, novel viruses often cause greater epidemiological and health hazards as the host’s immune system cannot effectively combat a pathogen it has never seen (stay tuned for our next post!). Therefore, emerging infections create a significant challenge for scientists and public health officials, putting them under tremendous pressure to quickly elucidate the mechanisms underlying viral pathology and pinpoint avenues for antiviral treatments. This is well-illustrated by the ongoing SARS-CoV-2 pandemic (also known as COVID-19 or the novel coronavirus), which first began in November 2019 and has since garnered unprecedented global attention, motivating an estimated 50,000+ (at the time of this post) publications in just eight months.

So, how do scientists go about examining and characterizing emerging viruses?

It is important to note that newly discovered viruses are not a complete mystery; they likely belong to already classified virus families, which have been investigated before. For instance, SARS-CoV-2 is in the Coronaviridae family, viruses that have (+) ssRNA genomes and spiked surface proteins that give them a crown-like appearance (hence their name). Coronaviridae is also the source of the recent MERS and SARS (severe acute respiratory syndrome, 2003-present) outbreaks. Current scientists thus benefit from previous research focused on coronaviruses, leveraging characteristics that are conserved across viral species and host responses.

For example, all coronaviruses use cap-dependent mRNA translation to express viral genes, a process that is augmented by the SARS-CoV N protein. Targeting this viral protein or the host protein complex involved in SARS-CoV-2 protein biogenesis could inhibit translation of viral genes and subsequently hinder the production of new infectious particles. In addition, the coronavirus genome encodes for a polyprotein that must be processed by viral and cellular proteases to make functional protein units. It is possible that designing drugs against these proteases (especially the major viral protease 3CLpro) will inhibit infections, a hypothesis that had been previously proposed and received much attention in recent months. Beyond coronavirus-specific processes, viral strategies to subvert host cell functions – such as exploiting protein interactions, immune signaling pathways, membrane fusion machinery, or organelle structures – are often conserved across diverse human virus infections. Researchers can make use of these overarching themes to hypothesize and elucidate processes at the core of emerging virus biology.

In addition to pre-existing biological knowledge, virologists are well-equipped with technologies and methodologies that enable the discovery of viral disease mechanisms. As we recently highlighted, developments in “omics” approaches, including genomics, metabolomics, transcriptomics, and mass spectrometry (MS)-based proteomics, allow researchers to perform high-throughput characterizations of virus infections with unprecedented speed and accuracy. Our lab integrates these methods to examine virus-host dynamics during infections with critical human viruses, including herpesviruses (e.g., human cytomegalovirus (HCMV) and herpes simplex virus type 1 (HSV-1)), orthomyxoviruses (e.g., Influenza A), and togaviruses (e.g., Sindbis virus). In ongoing studies of the novel coronavirus, omic technologies – especially proteomics – have proven essential for unraveling the biological and clinical challenges presented by SARS-CoV-2.

Proteomic methods are largely utilized with the goal of identifying therapeutic targets en masse. For example, a recent study in Nature used affinity purification MS (AP-MS) to examine protein-protein interactions (PPIs) between host and viral proteins during infection. The authors uncovered over 300 high-confidence PPIs, and applied this knowledge to target the identified human proteins with approved drugs and clinical compounds, searching for antiviral effects. This approach identified translational inhibitors and small molecules binding to cell-surface receptors as antiviral candidates. Similar results were obtained in another proteomics investigation, whereby translational inhibitors were found to be potent inhibitors of SARS-CoV-2 replication. Notably, these drugs have been utilized in pharmacological settings against other coronaviruses like SARS-CoV-1 and MERS-CoV. To rapidly discover novel drugs for SARS-CoV-2, a group from ShanghaiTech University developed a systems-level assay that combined information on molecular protein structure with computational drug design and high-throughput enzymatic screening. The investigators screened over 10,000 small molecules against the SARS-CoV-2 Mpro protease, quickly identifying numerous promising candidates for disease intervention.

In parallel, researchers have employed omics approaches to accelerate COVID-19 disease detection and diagnosis. A recent effort combined proteomics with metabolomics to sensitively profile changes in COVID-19 patient sera, allowing for the development of a computational disease progression model that can predict the progression of COVID-19 from a mild to severe state. Similar approaches promise to provide clinical and medical professionals with much needed tools for the proper treatment of emerging diseases. In the specific case of SARS-CoV-2, future studies aimed at characterizing protein post-translational modifications, organelle remodeling, and virus assembly, among many others, will benefit from utilizing proteomic technologies to piece together a global picture of virus pathology and disease progression.