Study of genetic and immunological events in Lynch syndrome progression to colorectal cancer

Colorectal cancer (CRC) is the 3rd most common cancer in the world, with around 3% of cases occurring due to a hereditary autosomal dominant disease called Lynch syndrome (LS). This non-polyposis condition is identified by a germline monoallelic mutation or hypermethylation in one of the mismatch repair (MMR) genes (MLH1, MSH2, MSH6 and PMS2). MMR deficiency (MMR-d) is reached through somatic loss of function in the remaining healthy allele and leads to a gain or loss of repeats in microsatellite tracts, which ultimately can develop into microsatellite instable (MSI) cancer. Identified LS patients stay on surveillance throughout their lifetime, undergoing colonoscopies every few years. No increase in adenoma growth is seen between LS patients and other non-predisposed patients, but the rate of carcinoma incidence is vastly increased with a 20-80% lifetime CRC risk in LS compared to ~5% in the general population. Due to this there has been much interest in improving predictive techniques, early detection and chemoprevention in LS. To address these issues, the early events leading to MMR-d as well as continuing evolution to carcinoma must be fully understood.

My project aims to study the earliest events in LS patients that lead to the development of CRC. Some LS patients display no evidence of polyp formation prior to cancer, indicating the traditional adenoma-carcinoma colorectal pathway may not occur in these patients. In addition, complete MMR-d has been recorded in non-neoplastic LS colonic crypts. Together this implies an irregular non-classical root to cancer formation in LS patients. The immune landscapes of LS CRCs are distinct from both sporadic MSI CRCs and CRCs occurring in other familial inherited syndromes. Interestingly this unique immune landscape is similar in both MMR heterogenous and MMR-d biopsies from LS carriers which may imply changes in immune activation early in life, before any detectable neoplasia. Once MMR-d is gained in LS patients there is an increase in mutational burden, neoantigen presentation and FOXP3+ regulatory T cells.

Aims:
1. To determine the events, and in what order, occur in addition to MMR-d in LS patients in the normal-adenoma(?)-cancer pathway. Does immune infiltrate need to be altered to a suppressive regulatory phenotype for progression to occur?

2. Investigate how essential the order in which these events occur, or is it the accumulation of the events that is important?

3. Study the ongoing progression of neoantigen presentation throughout normal-adenoma(?)-cancer pathway. Are there certain times in the timeline that neoantigen amount jumps and what event exactly does this coincide with?

Hypothesis: Lynch Syndrome patients have previous events creating a distinct environment favourable to cancer before any detectable presence of MMR-d related lesions occur.

Clinical relevance: By understanding the early events that occur in LS, even before any presentation of abnormal tissue, a better strategy of prevention and surveillance can be determined for LS carriers.

These aims will be investigated using human LS normal, polyp and cancer samples. Staining for MMR-d and a panel of immune markers throughout the tissue will be carried out. Analysis for the spatial organisation of immune cells in relation to MMR-d cells will be performed as well as analysis of clonal expansion areas in MMR-d crypts as a predictor of subpopulation fitness and time of mutation. Laser capture of individual crypts will allow for whole genome sequencing to identify neoantigen presentation and mutational burden in correlation to immune landscape and MMR-d throughout the timeline of patient samples.