Sharma Group: Comparative Analysis of TCR-Mediated Cytotoxicity Using Genome-Wide CRISPR Screens to Identify Host Factors in Natural vs. Vaccine-Induced Immunity

Supervisor: Sumana Sharma

This PhD project aims to systematically identify cellular factors that regulate T cell cytotoxicity by comparing matched TCR clones derived from natural viral infections versus vaccination responses, using genome-wide CRISPR knockout screens that the Sharma group specializes in, conducted in both target cells and directly within the T cells themselves. The research addresses a fundamental gap in our understanding of how immunological context shapes T cell programming and function. While TCRs with identical sequences can arise in different contexts, their effector functions may be influenced by distinct cellular factor networks that have not been comprehensively mapped. Through close collaboration with the Dong group, who have previously identified distinct clones of TCRs from individuals with documented natural viral infections and from vaccinated individuals with the same viral specificities, we will focus on epitopes from SARS-CoV-2. These matched TCR clones will undergo comprehensive CRISPR knockout screens targeting approximately 19,000 genes, with functional readouts measuring cytotoxicity, degranulation markers, and cytokine production to identify which cellular factors are essential for optimal T cell effector function. Parallel screens will also be conducted in target cells to identify host factors that distinguish the different clones.

About the Research 

This research could reveal fundamental molecular differences between naturally-acquired and vaccine-induced immunity, potentially discovering novel metabolic pathways, signaling networks, or regulatory factors that are differentially active across immunological contexts. The findings may explain why natural infection sometimes provides broader protection than vaccination, identify missing components in vaccine-induced responses that could be therapeutically targeted, and uncover previously unknown cellular factors that fine-tune cytotoxic efficiency. Downstream validation will include utilization of network-based computational tools to reconstruct pathway differences between the different modalities from different clones and reprogramming of clones using targets identified from the screen to generate novel signal transduction networks that differ between natural and vaccine-derived T cells. These insights could lead to enhanced vaccine strategies that better mimic natural immunity, improved T cell therapies through targeted manipulation of identified pathways, and development of functional biomarkers for predicting immune responses and vaccine efficacy.

This project is not suitable for part-time research.

Training Opportunities 

• Genome-wide screening
• Primary T cell culture and manipulation
• Computational network-based approaches
• Flow cytometry

Students will be enrolled on the MRC Weatherall Institute of Molecular Medicine DPhil Course, which takes place in the autumn of their first year. Running over several days, this course helps students to develop basic research and presentation skills, as well as introducing them to a wide range of scientific techniques and principles, ensuring that students have the opportunity to build a broad-based understanding of differing research methodologies.

Generic skills training is offered through the Medical Sciences Division's Skills Training Programme. This programme offers a comprehensive range of courses covering many important areas of researcher development: knowledge and intellectual abilities, personal effectiveness, research governance and organisation, and engagement, influence, and impact. Students are actively encouraged to take advantage of the training opportunities available to them.

As well as the specific training detailed above, students will have access to a wide range of seminars and training opportunities through the many research institutes and centres based in Oxford.

The Department has a successful mentoring scheme, open to graduate students, which provides an additional possible channel for personal and professional development outside the regular supervisory framework. We hold an Athena SWAN Silver Award in recognition of our efforts to build a happy and rewarding environment where all staff and students are supported to achieve their full potential.

Additional Supervisors 

1. Tao Dong

2. Yanchun Peng 

Publications