Targeting noncanonical epitopes to develop novel immunotherapies for leukaemia

Primary supervisor: Michele Mishto, King’s College London

Secondary supervisor: Rob Sellar, UCL

Project

Recent research has shown that proteasome-generated spliced epitopes represent a sizeable portion of the full set of antigenic peptides presented by cancer cells to CD8⁺ T cells. Few labs have attempted the development of novel immunotherapies against cancer targeting these noncanonical epitopes.

The overall objective of this project is to investigate the antigenicity and immunogenicity of recently identified spliced epitope candidates and their potential use in developing novel immunotherapies in acute myeloid leukaemia (AML), acute lymphoblastic leukaemia (ALL) and chronic myeloid leukemia (CML).

The student will work with the Mishto and Sellar labs and their international colleagues in a multi-disciplinary multi-omics multi-centre project.

This project builds on preliminary work done by a PhD student in the Mishto lab who is completing the PhD project that was a seminal project  and built a legacy in the Mishto lab.

In this CRUK-CoL Centre project, the student will further investigate the epitope candidates already identified using isolated TCRs, and will identify new epitope candidates and isolate specific TCRs applying the same strategy on new neoantigens associated to ALL-AML-CML.

The project relies on the expertise of the Mishto lab in HLA-I antigen presentation pathway (APP), which is among the leading groups studying proteasome-generated spliced epitopes, and Sellar lab, who combine clinical and experimental research on leukemia, in addition to the assisting in the curation of the UCL biobank for leukaemia and the generation of patient derived organoid (PDO) models of normal and malignant haematopoeisis.

The PhD student will:

• Investigate the antigenicity and immunogenicity of the ALL-AML-CML-associated noncanonical epitope candidates already identified in Mishto lab by performing: (i) ex vivo assays on leukemia patient PBMCs, (ii) cytotoxicity assays using CTL clones and TCR-transduced T cells, (iii) in cellular assays to determine the key steps of HLA-I APP that can impact on the epitope presentation.
• Identify novel proteasome-generated spliced epitope candidates derived from other ALL-AML-CML-associated neoantigens already identified in Mishto lab. To this end, both in-house bioinformatics and computational biology tools as well as in vitro and in cellular methods will be applied [1-3].
• Isolate and clone CD8+ abTCRs specific for the new proteasome-generated spliced epitope candidates derived from ALL-AML-CML-associated neoantigens.
• Investigate the potential cytotoxicity of abTCRs specific for proteasome-generated spliced epitopes against ALL-AML-CML cell PDOs with a long-term prospective of using them in developing novel immunotherapies against AML. In the PDOs, investigate potential resistance mechanisms to abTCR based therapies and explore approaches to mitigate these [4,5].
• Potentially, performing in vivo experiments to test the therapeutical value of targeting the ALL-AML-CML-associated epitopes with TCR T cell therapy. This part of the project is not mandatory and depends on the PhD student’s preference.

Candidate background

The project is highly multi-disciplinary, therefore the student should be motivated to carry out both dry lab and wet lab experiments. The supervisors have all expertise to support the student’s learning curve.  Other members of the labs will be involved in the project to carry out some specific tasks, which will be coordinated by the student.

Potential placements

1. Juliane Liepe, MPI Göttingen (Germany)
2. Benny Chain, Institute of Infection, Immunity and Transplantation, UCL
3. Rob Sellar, Cancer Institute, UCL

References

1. Soh WT, Roetschke HP, Cormican JA, Teo BF, Chiam NC, Raabe M, Pflanz R, Henneberg F, Becker S, Chari A, Liu H, Urlaub H, Liepe J*, Mishto M*. Degradation of proteins by human 20S proteasomes sheds light on the interplay between peptide hydrolysis and peptide splicing. Comm. 2024 Feb 7;15(1):1147. doi: 10.1038/s41467-024-45339-3.
2. Liepe J, Sidney J, Lorenz FK, Sette A, Mishto M. Mapping the MHC class I spliced immunopeptidome of cancer cells. Cancer Immunol Res. 2019 Jan;7(1):62-76. doi: 10.1158/2326-6066.CIR-18-0424. Epub 2018 Nov 13. PubMed PMID: 30425108.
3. Liepe J, Marino F, Sidney J, Jeko A, Bunting DE, Sette A, Kloetzel PM, Stumpf MP, Heck AJ, Mishto M. A large fraction of HLA class I ligands are proteasome-generated spliced peptides. Science 2016 Oct; 354(6310): 354-358. DOI: 10.1126/science.aaf4384.
4. Sellar RS, Sperling AS, Słabicki M, Gasser JA, McConkey ME, Adams DN, Zou C, Miller PG, Boettcher S, Lin AE, Sandoval B, Kovalcik V, Koeppel J, Fink EC, Yang L, Chan A, Pokarel S, Bergstrom E, Burt R, Udeshi ND, Carr SA, Chen C-W, Ebert BL. Degradation of GSPT1 causes TP53-independent cell death in leukaemia while sparing normal hematopoietic stem cells. Journal of Clinical Investigation 2022; 132(16).
5. Słabicki M, Kozicka Z, Petzold G, Li YD, Manojkumar M, Bunker RD, Donovan KA, Sievers QL, Koeppel J, Suchyra D, Sperling AS, Fink EC, Gasser JA, Wang LR, Corsello SM, Sellar RS, Jan M, Gillingham D, Scholl C, Fröhling S, Golub TR, Fischer ES, Thomä NH, Ebert BL. The CDK inhbitor CR8 acts as a molecular glue degrader that depletes cyclin K. Nature 2020;585(7824(:293-297). doi: 10.1038/s41586-020-2374-x