The proteomic, immune, and antigenic profiling of colorectal cancer for the design of CAR-T cell therapies

Abstract

Colorectal cancer (CRC) is forecast to become the leading cause of cancer and cancer-related deaths by 2040. Although it predominates in older patients, there has been a rise in young onset disease. Efforts have been made to improve prognostication methods; however, none have been able to standalone independent of the AJCC classification system. Chimeric antigen receptor T cell (CAR-T cell) therapies have significantly improved survival in haematological malignancies, and if rationally designed have the potential to improve outcomes for solid organ cancers including CRC. The aim of this thesis was to design a signature that predicts relapse in CRC and to characterise the antigenic, immune and proteomic landscape of CRC for the purpose of rational CAR-T cell design.

Utilising a large cohort of early-stage CRC between 2009-2020 from a tertiary referral centre, 495 patients treated for stage II and III CRC, and 145 patients treated for locally advanced rectal cancer (LARC) were identified. High-risk groups were identified including Tumour stage 4 (T4), mucinous histology, young onset rectal cancer (yRC), MSI-H LARC and mucinous histology.

A PILOT project using SWATH proteomics and Imaging Mass Cytometry identified immunosuppressive pathways and proteins in CRC for potential targeting, with CAR-T cells against EPHA2 and CEACAM5 offering therapeutic options. A signature combining EPHA2, CEACAM5 and GDF-15 for targeting with next generation CAR-T cell therapies could prove effective and improve durable activity, whilst eliminating life-threatening toxicities.

A 19-protein signature was discovered and was prognostic for Relapse Free Survival (hazard ratio (HR) 2.7, 95%CI: [2.24 – 3.18]; p < 0.0001) and overall survival (HR 1.6, 95%CI [1.40, 1.76). Significant heterogeneity in pathways and proteins was seen in this cohort of stage II and III CRC, paving the way forward for novel CAR-T cell design and rational clinical trial designs for the high-risk groups.