Identification of tumour-specific spliced epitopes to target large cohorts of cancer patients by immunotherapy

Identification of tumour-specific spliced epitopes to target large cohorts of cancer patients by immunotherapies Background Targeting CD8+ T cells to recurrent tumour-specific mutations can profoundly contribute to cancer treatment.

To promote this, I advocate targeting tumour-specific spliced epitopes (TSSEs), which overcome limits on antigen sequence diversity, thereby potentially treating a substantially larger patient cohort.

Spliced epitopes are naturally produced by proteasomes through reshuffling the antigen sequence and although they have been increasingly studied in infection and autoimmunity, they have been largely neglected in cancer immunotherapy. Aims My Aim is to identify and validate TSSEs as targets of anti-cancer immunotherapies for large numbers of patients.

I shall employ a multi-disciplinary approach including: (i) the systematic identification and characterisation of TSSEs which carry BRAF, KRAS and NRAS mutations; (ii) the generation and validation of TSSE-specific T cells and TCRs suitable for adoptive T cell therapy (ATT); (iii) the quantitation of TSSE antigenicity in cancer patients.

Our preliminary results show that we can almost triple the potential melanoma and pancreatic cancer population treatable with ATT by targeting TSSEs identified in this project.

Methods TSSE identification and characterisation will be studied at a biochemical and cellular level by combining in silico and in vitro methods which I have co-developed over the last decade.

Specific CD8+ T cell clones and their TCRs will be isolated from the peripheral blood of patients with melanoma and pancreatic cancer, and the lymphocyte responses to spliced epitopes compared between patients and controls.

Thereupon, the efficacy of TSSE-specific CD8+ T cell clones to selectively recognise and eradicate cancers will be tested in vitro and in xenograft tumour models.

How the results of this research will be used The project will: 1. generate a computer-based method for the prediction of spliced peptide generation. 2. identify spliced epitopes carrying selected tumour-specific mutations that can be employed in different immunotherapeutic strategies; 3. define the features of naturally-occurring adaptive immune responses against TSSEs in cancer cells, potentially impinging upon the efficacy of immunotherapies such as checkpoint blockade; 4. isolate CD8+ T cell clones and their TCRs reactive to TSSEs, which can be used in adoptive T cell therapies (ATTs); 5. build a foundation for clinical trials using ATTs against melanoma, pancreatic adenocarcinoma, colon carcinoma and other tumours carrying mutations that are presented as spliced epitopes.