Research Opportunities

There is a need for new drugs to combat viruses that threaten our health. Most existing antivirals inhibit virus attachment/entry or target critical enzymes, and new antiviral targets are needed to develop novel treatments and counter antiviral resistance. One key process in the life cycle of many viruses is the formation of dynamic organelles called viral factories. There is increasing evidence that some viral factories form via liquid-liquid phase separation (LLPS), including SARS-CoV-2, influenza, and measles virus. These compartments concentrate viral replication enzymes and sequester replication intermediates from the immune sensors. Targeting the physicochemical process of phase separation is an emerging paradigm that may underlie the discovery of novel, broad-spectrum antivirals, but this can only be realised by first understanding how viral factories form. This research project will focus on dissecting the physicochemical properties of these viral condensates to understand how their dynamic conformations and posttranslational modifications that affect charge mediate assembly of viral factories, and in doing so, identify targets for future therapeutic intervention. To quantitatively describe the formation of these condensates, we will examine the observed phase transitions of binary and tertiary mixtures of recombinantly produced viral proteins, as well as viral RNAs in vitro using the recently developed high-throughput microfluidics platform PhaseScan. These findings will lead us to define a new model of viral replicative condensate formation that addresses protein-specific attributes (posttranslational modifications, conformation), and their highly selective RNA composition (partitioning of cognate viral transcripts and exclusion of non-viral RNAs). The insights gained from these approaches will underlie the search for compounds that could serve as drug templates for prospective therapies for RNA viruses and improve our fundamental understanding of the synergistic interactions of viral proteins that spontaneously form complex condensates that are involved in viral replication.

This project will provide an excellent research environment that will foster the future development of the PhD candidate through extensive multi-disciplinary training in
i) microfluidics;
ii) protein biochemistry;
iii) biophysics of condensates;
iv) machine learning approaches required for bespoke data analyses.

This project will provide a unique training environment required for training next-generation biochemists interested in exploring biomolecular condensates and their roles in viral replication and assembly, with an ultimate goal of identifying new druggable antiviral targets.

Evolution has produced an arms race between viruses and the cells they infect. Studying this battle provides key insights into cell biology and immunology, as well as the viruses themselves. It may even lead to the development of novel therapeutics. The Matheson lab therefore focuses on two pandemic viruses with a major impact on human health: HIV and SARS-CoV-2.  

We have previously used unbiased proteomics to quantify dysregulation of hundreds of proteins and processes in infected cells, and now aim to understand the importance of these targets for both viral pathogenesis and normal cellular physiology. Because HIV regulates numerous cell surface amino acid transporters, we are particularly interested in amino acid metabolism and protein biosynthesis.  

Depending on the interests of the student, this project will therefore focus on either (1) an orphan cell surface amino transporter downregulated by SARS-CoV-2 infection of respiratory epithelial cells or (2) an ancient metabolic enzyme regulating ribosomal frame shifting depleted by HIV infection of primary human CD4+ T cells.  

In either case, the aims will be to: validate the target in different systems; define the mechanism of viral regulation; determine the functional effects of target depletion in biochemical and cell biological assays; and characterise the impact of target depletion on viral infection. Opportunities will be available to conduct further proteomic screens, perform ribosomal profiling and/or stable isotope-based metabolomics.   

The project will provide training in a wide range of molecular and biochemical techniques, whilst allowing the student to explore an important aspect of the host-virus interaction. The Matheson lab is based in the brand new Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), including the largest academic Containment Level 3 (CL3) facility in the UK. The student will be supervised by an experienced postdoc in a friendly, supportive group. 
 

Antiviral restriction factors (ARF) are a critical element of cellular innate immunity, representing the first barrier to viral infection that can determine outcome. We aim to identify and characterise novel ARF and their viral antagonists, since therapeutic interruption of viral antagonism can enable restoration of endogenous antiviral activity.

We employ a number of human pathogens, in particular Human Cytomegalovirus (HCMV), Monkeypox virus (MPXV) and its vaccine, Modified Vaccinia Ankara (MVA). Our systematic proteomic analyses determine which cellular factors each pathogen targets for destruction, since we have shown these to be enriched in novel ARFs. For example, we recently developed a multiplexed proteomic technique that identified proteins degraded in the proteasome or lysosome very early during HCMV infection (Nightingale et al, Cell Host & Microbe 2018). A shortlist of 35 proteins were degraded with high confidence, and we have since shown that several are novel ARF, with characterisation of these factors forming ongoing projects. Application to MVA infection indicated further candidates, and identified novel mechanisms of vaccine action (Albarnaz et al, in review, https://www.researchsquare.com/article/rs-1850393/v1). Furthermore, interactome screens can identify the viral factor(s) responsible for targeting each ARF, and indicate mechanism (Nobre et al eLife 2019).

This project will now identify and characterise critical pan-viral ARF, which can restrict diverse viruses. For the most potent, we will determine both the mechanism of restriction and the mechanism of virally mediated protein degradation. In order to prioritise the most important factors, there will also be the opportunity to use novel multiplexed proteomic screens.

Retroviruses, flaviviruses and coronaviruses are important pathogens capable of causing serious human disease. To replicate and disseminate infection, these viruses hijack host cell machinery, including organelles such as the endoplasmic reticulum, the Golgi apparatus, lipid droplets and the nucleus to generate progeny virions. Sensors within the innate immune system detect virus-induced membrane reorganization, identify virus weak spots, and influence disease progression in this complex virus-host interplay. This project focuses on the innate immune response that specifically targets virus replication and translation complexes (RTCs) anchored at the membrane of cell host organelles. RTCs isolated from these sites will be studied using molecular and cell biology, in combination with bioinformatics, structural biology and high resolution imaging to design novel antiviral interventions.

The formation of infectious HIV-1 particles requires the incorporation of Env glycoproteins during the assembly process, with Env mediating binding of newly released virions to target cells and subsequent entry via fusion between viral and target-cell membranes. The interaction between the MA domain of Gag and gp41 of Env plays a central role in Env incorporation into virions and in the activation of Env fusion activity, yet this interaction remains poorly understood at the biochemical and structural levels. In addition, recent structures of the MA lattice in both immature and mature HIV-1 particles implicate a maturation-induced rearrangement of MA the lattice. This opens the possibility that MA-gp41 interactions are dynamic, and change during the maturation process.

We aim to apply an array of biochemical, structural, super-resolution imaging, and virological approaches that will interrogate the MA/gp41 interaction and will provide novel insights into the mechanism and dynamics of Env incorporation into HIV-1 particles. A set of informative mutants, which display stabilized MA-MA and/or MA-gp41 interactions, will be used for structural studies,. Cryo-ET analysis of intact mature and immature virions will be performed to obtain structural data that will complement the information obtained with the MA/Gag assemblies. Predictions regarding potential sites of MA-MA and MA-gp41 interactions obtained from these structural studies will be tested in Env incorporation and virus replication assays. This combination of structural, biochemical, and virological studies will help to elucidate the mechanism of Env incorporation into HIV-1 particles and the subsequent process of particle maturation.

Human immunodeficiency virus type 1 (HIV-1) is the causative agent behind acquired immunodeficiency syndrome (AIDS) that currently has no cure or vaccine. While antiviral treatments are effective, the rise of drug-resistant strains has become a growing concern. HIV-1 primarily infects the immune system, targeting CD4+ T cells and macrophages and is a lentivirus known to be able to infect non-dividing cells, requiring it to exploit nuclear import mechanisms. This process is dependent on the viral capsid. The HIV capsid is a conical structure that houses the genomic material of the virus. It needs to be metastable in order to be protective while allowing timely disassembly (termed uncoating) to release its genome. The dynamics of the capsid nuclear import and uncoating are still unknown and are modulated by host dependency and restriction factors.

We aim to apply multi-imaging modalities to investigate uncoating and nuclear import of HIV. These will include super-resolution fluorescence microscopy (including the newest MINFLUX technology), Focused Ion Beam and Scanning electron microscopy (cryoFIB/SEM), cryo-electron microscopy and cryo-electron tomography (cryoEM/ET). The viral core and host factors will be fluorescently tagged, and infection will be monitored from viral attachment to nuclear import. The sample will be cryo-preserved and imaged by cryoEM/ET and cryoFIB/SEM. The combination of these imaging techniques, paired with molecular biology and virology tools, will yield unparalleled knowledge of the HIV infection process within the native cells, providing the framework for development of novel therapeutics targeting HIV infection in the future.

Infections by retroviruses, such as HIV-1, critically depend on the viral capsid. Many host cell defence proteins, including restriction factors Trim5α, TrimCyp and MxB, target the viral capsid at the early stages of infection and potently inhibit virus replication. These restriction factors appear to function through a remarkable capsid pattern sensing ability that specifically recognizes the assembled capsid, but not the individual capsid protein. Using cutting-edage cryoEM technologies, we aim to determine the molecular interactions between the viral capsid and host restriction factors that underpin their capsid pattern-sensing capability and ability to inhibit HIV-1 replication. Specifically, we will combine cryoEM and cryoET with all-atom molecular dynamics simulations to obtain high-resolution structures, together with mutational and functional analysis, as well as correlative light and cryoEM imaging of viral infection process, to reveal the essential mechanism for HIV-1 capsid recognition and inhibition of HIV-1 infection. Information derived from our studies will allow to design more robust therapeutic agents to block HIV-1 replication.

The aim of this project will be to apply Next Generation Sequencing (NGS) approaches simultaneously to both host and the HIV provirus. The candidate will apply and improve methods to produce full-length viral haplotype and integration site data (already developed in the lab) from cohorts of individuals with treated early HIV infection, many of whom will receive experimental interventions and stop antiretroviral therapy.

Simultaneously, unbiased transcriptomic profiling (RNASeq) and analysis of DNA accessibility (ATAC-Seq) will be incorporated to allow a global interrogation of viral and host genomics, with potential to extend this to single cell analyses. Following method development, clinical samples from UK cohorts will be analysed to characterise the reservoir and to inform the source of rebound viraemia on treatment interruption. The work will therefore have both a cross-sectional and longitudinal component, promising significant analytical power. Working collaboratively with other group members and projects to link cell phenotype and subset with viral phylogenetics to identify the source of viraemia will be an important part of the work.

The candidate would be expected to have interests in both the laboratory wet-lab and bioinformatic components of the project, to achieve a unified problem-solving approach.

1. Biomarkers of the HIV reservoir and remission in primary HIV infection
2. Simultaneous host and pathogen 'omics to interrogate the HIV reservoir
3. Microfluidic and Lab-on-a-Chip approaches to characterising the HIV reservoir

*This project is available for the 2021 Oxford-NIH Pilot Programme*

The mortality rate for COVID-19 pandemic has been two-fold higher in men than women. Similar observation extends to susceptibility and outcome of most other infectious diseases. For instance, after initial Hepatitis C Virus infection women are 2-3 times more likely to spontaneously clear the virus without any interventions and in HIV infection females are 5 times more likely to achieve elite control (complete suppression virus without therapy) than men. However, a consequence of the more vigorous immune response observed in females is more immunopathology and auto-immune diseases (such as lupus) in women than men. For the same reasons, females make stronger immune responses to vaccines but suffer more adverse events. Despite large evidence for sex differences in autoimmune diseases and susceptibility and outcome of infectious diseases, data addressing the biological mechanism are remarkably scarce.

In this project you will use computational and experimental methods to probe differences in immune system that lead to sex differences in infectious diseases. We will investigate this question across many infections including HCV, HBV, HIV and COVID-19. You will start with analysing the available RNA-seq and genomic data from our cohorts and other public databases to understand the role of heterogeneity in X chromosome inactivation in female immune cells and the transcriptional consequence and its contribution to better outcome in infectious diseases. In the next stage you will stimulate male and female immune cells with different immunogens and perform single cell RNA-sequencing to evaluate differential responses across distinct cell types and their association with sex. The project will also use samples and data from vaccine clinical trials. The baseline samples will be compared to the post-vaccination samples and differences in immune systems between sexes will be investigated.

This project will investigate mechanisms of assembly, secretion and immune subversion adopted by (+)RNA viruses, with a particular emphasis on Dengue/Zika from the flavivirus and SARS-CoV-2 from the coronavirus families. Current understanding on how small (+)RNA viruses assemble and spread from cell to cell while evading innate and cellular immune responses is limited. Virus-infected cells induce selective autophagy of lipid droplets, which is accompanied by massive reorganisation of the host secretory pathway, but downregulate MHC-I and II restricted antigen presentation and often interferon production.

We have identified host factors that are targeted by viral proteins to induce autophagy-mediated LD hydrolysis (lipophagy) and unconventional secretory processes1,2. Collectively they are crucial for formation of viral replication compartments, assembly and cell-to-cell spread of virus progenies. We will apply CRISPR/Cas9 gene editing technology combined with biochemical and cell biological methods and functional assays to investigate how specific genes affect virus assembly and secretion. 

Infection by Dengue/Zika and SARS-CoV-2 also results in dramatic reduction of MHC-I and II restricted antigen presentation in monocytes and monocyte-derived cells. We will address how these viruses subvert innate and cellular immune responses to drive pathogenesis3,4. We aim to delineate biosynthesis, assembly, transport and turnover of MHC-molecules to define the specific steps targeted by these viruses. We will test E3 ligase candidates that are induced and copurify with MHC-I and II from virus infected cells, that may degrade or mis-sort MHC molecules to evade host immunity. We will combine quantitative mass spectrometry with complementary approaches in biochemistry, cell biology, immunology and virology to investigate the interplay of host cellular pathways such as autophagy, with that of virus biogenesis, and their mode of host immune evasion.

Viruses are obligate parasites that have evolved to manipulate their host to their advantage. Chronic viral infection of the liver is a global health problem, with over 300 million individuals infected with hepatitis B (HBV) or C (HCV) virus that causes liver disease which can progress to liver cancer. Viral hepatitis-related liver disease is the number 4 disease-related killer worldwide and is associated with more than 1 million deaths/year, highlighting an urgent need for new curative treatments. We recently discovered that low oxygen environments, naturally found in the liver, enhance HBV replication at several steps in the viral life cycle. Similar condition may apply to HCV replication. Cellular response to low oxygen is regulated by a family of oxygenases and hypoxia inducible factors (HIFs) that control genes involved in energy metabolism and other cellular processes. This project will study the role of hypoxic signaling and related metabolic pathways in HBV or HCV replication and their impact on pathogenesis, immune based and epigenetic therapies.

The successful candidate will investigate the molecular mechanisms underlying these observations. In particular, we will (i) identify the role of HIFs in HBV cccDNA biogenesis, transcription and metabolism, and production of infectious particles, and conduct comparative studies in HCV replication (ii) analyze how these host-virus interactions are shaped by the tissue microenvironment, genetic manipulations and metabolic parameters. The project has basic and translational research components and applies state-of-the-art technologies, tools and model systems to study HBV infection and its mechanism of disease. Taken together, this exciting project builds on strong preliminary results and existing expertise that may lead to new therapeutic targets and antiviral development.

*This project is available for the 2021 Oxford-NIH Pilot Programme*

Some of the most globally impactful diseases are caused by emerging and re-emerging viral pathogens. We have a long-standing collaboration with Vincent Munster at the NIH, investigating disease pathogenesis and developing vaccines against a number of outbreak pathogens.
 
This project represents an opportunity to join this world-class team to advance these works, investigating the mechanisms of disease, deriving correlates of protection, testing new therapeutic interventions and deriving structural determinants of disease through collaboration with Prof. Thomas Bowden.

Influenza A virus imposes a significant socio-economic burden on humanity.  Vaccination is effective in only 60% of individuals, even under optimal circumstances.  The difficulty stems from the remarkable ability of influenza A virus to evade existing immunity.  IAV’s error prone polymerase enables the rapid antigenic evolution of the two virion surface glycoproteins, neuraminidase (NA) and hemagglutinin (HA).  Since the most potent antibodies (Abs) at neutralizing viral infectivity are directed the HA and NA globular domains, amino acid substitutions in these regions enable IAV to evade Ab-based immunity.  The project focuses on understanding the “immunodominance” of Ab responses to HA and NA in humans.  Immunodominance describes the strong tendency of the immune response to respond to complex antigens in a hierarchical manner, with higher ranking, “immunodominant” antigens potentially suppressing (“immunodominating”) responses to “subdominant” antigens.  By focusing responses on single antigenic sites, it is likely responsible for enabling influenza A virus to evade immunity by allowing the virus to sequentially alter its antigenicity.