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Paresh Vyas


This exciting project brings together laboratories with established international reputations in haemopoiesis, the biology and treatment of AML (Prof Vyas), protein engineering, antigen-T cell receptor interaction and T cell responses (Dr Fernandes, Prof Gillespie and Dr Dushek). The overall aim of the project is to study in detail how tumour peptides bind HLA-II and how peptide-HLA-II antigens bind to the T cell receptor (TCR) to activate T cell responses. In contrast to well-studied antigen-HLA-I binding and T cell activation, much still remains to be understood about functionally important peptide-HLA-II (pHLA)-TCR interactions. The work will lead to development of novel TCR-based therapies for the most common aggressive adult human leukaemia, AML.  

By studying AML patients cured from an allogeneic stem and immune cell transplant, we have identified novel pHLA antigen targets on patient AML cells and the T cell receptors that recognise those targets. Interestingly, the bulk of these pHLA targets are HLA-II restricted and correspondingly elicit CD4 cytotoxic T cell responses. This project will focus on a limited number of pHLA antigens we have identified and characterise the detailed mechanisms of pHLA-II-TCR interactions through three aims: 

1. Characterisation of HLA-II binding to alloreactive peptide Using molecular biology and protein engineering methods the applicant will express soluble pHLA-II with varying peptide lengths and study the biophysical properties of peptide-HLA-II binding and compare this to computationally derived prediction of peptide-HLA-II binding. By mutating peptide resides the applicant can identify which peptide residues are critical for binding. This work will be combined with structural studies in Aim 3.

2. Characterisation of TCR binding and crossreactivity to pHLA-II antigen. Using molecular biology and protein engineering methods the applicant will express soluble TCR and test the biophysical properties of binding to pHLA-II to TCR. By mutating TCR resides the applicant can identify which TCR residues are critical for binding. If time permits, the applicant will generate a large, unbiased, peptide-MHC library for yeast display to determine the TCR crossreactivity of wild-type and engineered TCRs. Finally, for select TCRs that bind pHLA-II the mode of T cell activation and need for co-stimulation will be studied. This work will be combined with structural studies in Aim 3.

3. Structural studies of TCR-PHLA-II binding The data in Aims 2 and 3 will be greatly strengthened by structural studies of pHLA-TCR interaction. The applicant will take select soluble p-HLA-II antigens and cognate TCRs from aims 2 and 3 collaborate with a structural biology group to enable them to make crystals for structural studies using a range of structural resolution methods. 

The combination of Aims 1-3 will provide detailed insight into the mechanisms of p-HLA-II binding and the binding of pHLA-II antigens with TCRs.

Translational Potential. This project aims to identify the optimal pHLA antigens and TCRs for either TCR engager therapy or TCR T-cell therapies for AML and myeloid cancers.

Additional supervision may be provided by Dr Ricardo Fernandez (Nuffield Department of Medicine), Professor Geraldine Gillespie (Nuffield Department of Medicine) and Dr Omer Dushek (Dunn School of Pathology).

Please see the Radcliffe Department of Medicine (RDM) website for information about applications for a DPhil in Medical Sciences with groups based in RDM.



The DPhil student will be trained in: (i) fundamental aspects of immunology and specifically pHLA interactions and the binding of pHLA to TCR; (2) molecular biology, protein engineering and biophysical measurements of protein-protein interaction: (3) computational biology (4) structural biology. The training will be focussed on specific skill sets that are critical for developing immune therapies.

Key methods include:

  1. Protein engineering: complex molecular cloning, protein expression, protein purification, 
  2. Biophysical methods of measuring protein-protein interaction including surface plasma resonance. 
  3. Complex multi-colour flow cytometric analysis and FACS-sorting. All students will independently use flow analysers and sorters.
  4. Lentiviral and adeno-associated viral transduction of immune cells. 
  5. In vitro and in vivo assays of T cell function including biochemical analysis of TCR signalling.
  6. Crispr gene editing of cell lines and primary cells.
  7. Computational analysis including exposure to coding using Python and R.
  8. NGS libraries for RNA-seq, TCR sequencing, single cell genotyping+ ATAC-seq in single cells and highly purified cell populations. 

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.




Turkalj S, Jakobsen NA, Groom A, Metzner M, Riva SG, Gür ER, Usukhbayar B, Salazar MA, Hentges LD, Mickute G, Clark K, Sopp P, Davies JOJ, Hughes JR, Vyas P. GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells. Cell Stem Cell. 2023 May 4;30(5):722-740.e11. doi: 10.1016/j.stem.2023.04.012. PMID: 37146586


Labuhn M, Perkins K, Papaemmanuil E, Matzk S, Varghese L, Amstislavskiy V, Risch T, Garnett C, Hernandez, D, Metzner M, Kenndy, A, Iotchkova V, Stoilova, B, Scheer C, Yoshida K, Schwarzer A, Taub J, Crispino JD., Weiss MJ, Hayashi A, Taga T, Ito E, Ogawa S, Reinhardt D, Yaspo ML, Campbell PJ, Roberts I, Constantinescu S, Vyas P, HecklD, Klusmann JH. (Joint last authors). Mechanisms Of Progression Of Myeloid Preleukemia To Transformed Myeloid Leukemia In Children With Down Syndrome. Cancer Cell. Aug 12;36(2):123-138.310. Doi: 10.1016/j.ccell.2019.06.007 (2019). PMID: 31303423.


Quek L, David M, Kennedy A, Metzner M, Amatangelo M, Shih A, Stoilova B, Quivoron C, Heiblig M, Willekens C, Saada V, Peniket A, Bernard O, Agresta S, Yen K, MacBeth K, Stein E, Levine R,De Botton S, Thakurta A, Penard-Lacronique V and Vyas P. Clonal Heterogeneity in Differentiation Response and Resistance to the IDH2 inhibitor Enasidenib in Acute Myeloid Leukemia. Nature Medicine. Aug 24(8):1167-1177. Doi: 10.1038/s41591-018-0115-6. (2018). PMID: 30013198.