Untangling the mechanisms of presentation of unconventional epitopes to predict their immunogenicity and efficacy in anti-cancer immunotherapy

Primary Supervisor: Michele Mishto, King’s College London/ Francis Crick Institute

Secondary supervisor: Benny Chain, UCL

Project

Recent research has shown that unconventional epitopes – such as proteasome-generated spliced, cryptic or mutated peptides – represent a sizeable portion of the full set of antigenic peptides presented to CD8+ T cells. The CD8+ T cell response against these unconventional epitopes is at the cutting edge of the development of novel immunotherapies against cancer.

The overall objective of this project is to investigate the mechanisms of HLA-I processing and presentation (APP) of unconventional epitopes and their recognition by tumour infiltrating lymphocytes. The student will focus on proteasome-generated spliced peptides and cryptic peptides. He/she will develop and apply in silico/ in vitro pipelines for target discovery and in cellula/ ex vivo methods for their validation. The project will be embedded in a larger project on Head & Neck (H&N) cancer cohort and pediatric acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML) collected between KCL, UCL and Charité Berlin (D). The student will collaborate with the Mishto and Chain labs members and their international colleagues in a multi-disciplinary multi-omics multi-centre project.

This project builds on the expertise of the Mishto and Chain labs in HLA-I APP, who are leading figures in the research on unconventional epitopes and TCR recognition and prediction, respectively.

The PhD student will:

• Develop and refine strategies for identifying unconventional antigenic peptides candidates and integrating them with existing tools for predicting the peptide production, presentation and recognition by TCRs. Preliminary iterations of some of the predictors have already been developed and published by the two groups.
• Evaluate successive computational predictions using biochemical and immunological experimental in vitro and in cellula systems and ex vivo specimens from a large cohort of H&N cancer patients (HERD trial; Ng lab, UCL-KCL) and of childhood ALL and AML (Dr. Dillon, KCL and Dr. Dörr, Charité Berlin). This will include the analysis of proteomics, immunopeptidomics, molecular immunology assay, RNA transcriptomics and TCR sequencing data. This work will be carried out using systems that have already been developed in the Mishto and Chain labs as part of existing collaborations.
• Preliminarily investigate the potential application of the target unconventional epitopes and their cognate TCRs for immunotherapies against H&N cancers and childhood ALL and AML, such as adoptive T cell therapies and vaccinations.

Candidate background

The project is highly multi-disciplinary, therefore the student should be motivated in carry out both dry lab and wet lab experiments. The student should have a background and/ or skills in both biology and bioinformatics. Mishto and Chain labs have all expertise to supervise the student and help him/ her to acquire all required skills to complete the project. Furthermore, the project is well embedded in the research of the two labs, therefore 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 Research Placements

1. Liepe Lab, Max Planck Institute for Multidisciplinary Science, Göttingen (D)
2. Ng Lab, King’s College London
3. Centre od Excellence in Mass Spectrometry, King’s College London

References

1. Specht G, Roetschke HP, Mansurkhodzhaev A, Henklein P, Textoris-Taube K, Urlaub H, Mishto M*, Liepe J*. Large database for the analysis and prediction of spliced and non-spliced peptide generation by proteasomes. Sci Data. 2020 May 15;7(1):146. doi: 10.1038/s41597- 020-0487-6. PubMed PMID: 32415162.
2. Platteel ACM, Liepe J, Textoris-Taube K, Keller C, Henklein P, Schalkwijk HH, Cardoso R, Kloetzel PM, Mishto M*, Sijts AJAM*. Multi-level Strategy for Identifying Proteasome- Catalyzed Spliced Epitopes Targeted by CD8(+) T Cells during Bacterial Infection. Cell Rep. 2017 Aug 1;20(5):1242-1253. doi: 10.1016/j.celrep.2017.07.026. PubMed PMID: 28768206.
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. Epub 2016 Oct 20. PubMed PMID: 27846572.
4. Milighetti M, Shawe-Taylor J, Chain B. Predicting T Cell Receptor Antigen Specificity From Structural Features Derived From Homology Models of Receptor-Peptide-Major Histocompatibility Complexes. Front Physiol. 2021;12:730908. Published 2021 Sep 8. doi:10.3389/fphys.2021.730908
5. Joshi K, de Massy MR, Ismail M, […] Chain B. Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer [published correction appears in Nat Med. 2020 Jul;26(7):1148]. Nat Med. 2019;25(10):1549-1559. doi:10.1038/s41591-019- 0592-2