Clonal dynamics and mutational landscape of normal and cancerous tissues in cancer predisposition syndromes

Cancer predisposition syndrome, also called inherited cancer predisposition, or familial cancers are usually caused by pathogenic mutation(s) that are inherited from one or both parents and increase the risk of developing cancer at an earlier age compared to the risk for the general population. Although all the cells in the offspring carry the same pathogenic mutation(s), yet only some cell types are sensitive to these changes and transform into malignant tumours. Moreover, some tumours emerge early in these individuals (during childhood), such as sarcoma, while others take longer to form, such as breast cancer (usually it appears around the age of 20 and above). Despite the huge effort in the field to understand tumorigenesis in individuals with cancer predisposition syndromes, yet the cellular processes that cause malignant transformation in some cells but not in every single cell in the body remain unknown.

The aim of this study is to:
1) Generate a comprehensive mutational landscape across histological normal tissues of individuals with Li-Fraumeni syndrome, which is a type of inherited cancer;
2) Identify factors that cause an early tumour transformation in some cells compared to tumours that emerge later in life;
3) Investigate DNA modifications, such as changes in methylation, which may play a role in malignant transformation across different cell types.

The results from this study will help us better understand how malignant transformation occurs in some cells in individuals with cancer predisposition syndromes. The outcome will provide important insights into cancer risk and development in general.

This study aims to investigate the consequences of TP53 inactivation in malignant transformation, as well as in the development and maintenance of healthy tissues, using tumour and histologically-normal samples from Li-Fraumeni syndrome (LFS) individuals. LFS is a rare familial cancer syndrome caused by heterozygous germline pathogenic variants in TP53, which confer an increased risk of early onset cancer in diverse tissues of origin. Specifically, we will implement a multidisciplinary approach combining spatially-resolved, multi-omic technologies with single-clone and single-molecule resolution to delineate the patterns of mutations and mutational processes, clonal evolution and phylogenetic relationships of cells in LFS individuals. In Work Package (WP) 1 we will analyse samples from diverse histological structures (at least 25) collected post-mortem from ~10 LFS individuals. We will perform laser capture microdissection (LCM) combined with low-input whole-genome sequencing (WGS) on clonal structures, and NanoSeq on non-clonal tissues. The resulting data will allow us to study the consequences of pathogenic TP53 variants on the behaviour of normal cells and clones during life across diverse tissues. In WP2, we will apply WGS on multiple regions extracted using LCM from diverse tumours arising in LFS patients. We will primarily focus on studying the early events triggering the clonal expansion of malignant clones in an LFS background, and will compare the patterns of somatic alterations observed in benign clonal expansions with those leading to malignant transformation in LFS individuals, and in sporadic tumours driven by TP53 inactivation. In WP3, we will perform RNAseq and EMseq (low-input bisulfite sequencing) on the LCM samples collected in WP1 and WP2 to study transcriptional changes and epigenetic modifications in both histologically-normal tissues and tumour samples from LFS individuals.