Meta-analysis of genome wide functional screens to identify broad-spectrum antiviral and immuno-therapeutic targets

Precision Medicine Project - Meta-analysis of genome wide functional screens to identify broad-spectrum antiviral and immuno-therapeutic targets

Supervisor(s): Dr Richard Sloan, Dr Kenneth Baillie, Dr Finn Grey & Dr Robert Young
Centre/Institute: Centre for Inflammation Research

Background: 

The recent SARS-CoV-2 pandemic has exposed our need for broad-spectrum antiviral therapeutics and also our need to understand variable clinical outcomes in regards viral disease, morbidity and mortality. CRISPR/Cas9 knockout screens or similar have been extensively used in recent years to functionally identify required viral co-factors and regulating immune antiviral factors at the genome scale. Together these provide new leads in identifying viral therapeutic targets, susceptibility factors in patients, and targets for immunotherapy. Our laboratories have been engaged in such screening against viral pathogens such as influenza A virus, SARS-CoV-2 and Pseudorabies virus resulting in the identification of therapeutically tractable viral cofactors such as CMTR1.

However, screening via functional genomics inevitably reveals many potential targets. Equally, when further considering the extensive collective output of other laboratories world-wide engaged in parallel studies, there then exists a vast amount of extant functional data that is minimally exploited. In our own work, we have developed systematic rank aggregation tools to aid target prioritization from identified gene lists such as the meta-analysis by information content (MAIC) algorithm. More recently, we have further developed computational tools to automate ingestion of functional genomic data from published CRISPR/Cas9 screens. 

When these approaches are used together, we can combine the collective output of dozens of functional viral screens augmented with our own in-house unpublished data. This allows us to systematically identify the most consistently identified viral co-factors or restriction factors with increased study power. Analysis may be segregated according to virus type, family or at the pan-viral level, allowing nuanced insights to b made. Hits can be crossed referenced to GWAS data to help understand clinical outcomes, while hits can also be followed with systematic meta-analysis of published literature to determine novelty and therapeutic tractability. Collectively, systematic meta-analysis of functional genomic data allows us to identify the most robust targets for therapeutic identification and patient stratification across multiple functional data sets, while simultaneously being able to compare and contrast across virus types. This will allow the identification of novel broad-spectrum antiviral therapeutic approaches. 

Aims

The overall aim of this PhD project is to perform a meta-analysis of CRISPR/Cas9 viral functional screen data to identify, rank and then experimentally characterize host gene products that dictate the outcome of viral infection. This includes:

1.Meta-analysis to identify proviral and antiviral targets across published and in house functional genomic screens.

Meta-analysis tools such as MAIC and data ingestion tools will be employed to identify and initially rank  recurring proviral and antiviral targets of importance both across and within viral species. Priority will be given to viral pathogens of pandemic potential. 

2. Secondary ranking and filtering of viral targets through orthogonal omic-level data and meta-analysis. 

The target list identified will be further ranked and filtered according to identification in GWAS studies, evolutionary positive selection analysis, defined protein-protein interactions, transcriptomic profiles, and through systematic meta-analysis of published literature.

3. Experimental sub-screening and validation of identified proviral and antiviral targets using CRISPR/Cas9 knockout

Training outcomes

The project will involve a mix of both computational and wet lab approaches. The ideal candidate will have shown prior interest in computational approaches in biology, but full training will be given in the use of R, working in a Linux environment, use of in-house analysis tools (such as MAIC), transcriptomic analysis and data visualization. 

In the laboratory full training will be provided in cell culture, CRISPR/Cas9 screening approaches, viral culture, cloning and plasmi preparation, qPCR, and flow cytometry. At the end of this studentship the student will have all of the necessary skills to seamlessly transition between biological, clinical, and computational elements of biomedical science.

References

  1. Pairo-Castineira E , Rawlik K, Bretherick AD, Qi T, Wu Y, Nassiri I, McConkey GA, Zechner M, Klaric L, Griffiths F, ..., Baillie JK. GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19.
    Nature
    . (2023); doi:10.1038/s41586-023-06034-3
  2. Bo Li, Sara M. Clohisey, Bing Shao Chia, Bo Wang, Ang Cui, Thomas Eisenhaure, Lawrence D. Schweitzer, Paul Hoover, Nicholas J. Parkinson, Aharon Nachshon, Nikki Smith, Tim Regan, David Farr, Michael U. Gutmann, Syed Irfan Bukhari, Andrew Law, Maya Sangesland, Irit Gat-Viks, Paul Digard, Shobha Vasudevan, Daniel Lingwood, David H. Dockrell, John G. Doench, J. Kenneth Baillie & Nir Hacohen. Genome-wide CRISPR screen identifies host dependency factors for influenza A virus infection.
    Nature Communications
    . 11: 164 (2020)
  3. A genome-wide CRISPR/Cas9 screen reveals the requirement of host sphingomyelin synthase 1 for infection with Pseudorabies virus mutant gD–Pass. Hölpe, J. E. R., Grey, F., Baillie, J. K., Regan, T., Parkinson, N., Hoper, D., Thamamongood, T., Schwemmle, M., Pannhorst, K., Wendt, L., Mettenleiter, T. C. & Klupp, B. G. (2021)
    Viruses
    . 13, 8, 1574.
  4. Identification of Host Factors Involved in Human Cytomegalovirus Replication, Assembly, and Egress Using a Two-Step Small Interfering RNA Screen. Dominique McCormick, Yao-Tang Lin, Finn Grey.
    mBio
     9:3 (2018). https://doi.org/10.1128/mbio.00716-18
 

Apply Now

Click here to Apply Now

  • The deadline for 25/26 applications is Monday 13th January 2025
  • Applicants must apply to a specific project. Please ensure you include details of the project on the Recruitment Form below, which you must submit to the research proposal section of your EUCLID application. 
  • Please ensure you upload as many of the requested documents as possible, including a CV, at the time of submitting your EUCLID application.  

 

Q&A Sessions

Supervisor(s) of each project will be holding a 30 minute Q&A session in the first two weeks of December. 

If you have any questions regarding this project, you are invited to attend the session on TBC via Microsoft Teams. Click here to join the session.

This article was published on