Single-molecule multi-omics to study tumour heterogeneity and evolution

Cancer is a chiefly genetic disease, originating from the acquisition of somatic mutations in cells throughout our life. While most of these mutations are innocuous passengers, a handful unlock the typical hallmarks of cancer. The latter endow a cell with a fitness advantage relative to neighbouring cells, leading to a clonal outgrowth. Clonal expansions can be shaped by the evolutionary processes of selection and drift, which act on the often plastic phenotypes of the malignant cells and the extensive genetic variation generated within them by ongoing mutational processes. While recent advances in long single-molecule sequencing now allow us to explore complex ‘omics variation such as chromosomal rearrangements or splicing, single-cell techniques enable profiling of cell type heterogeneity at an unprecedented scale. Moreover, multi-omics information from the same molecule or cell connects variation in one ‘omics layer to changes in another, enabling development of a functional view of tumour evolution in the context of its microenvironment. In this project, we will analyse and integrate long-read and single-cell multi-omics data derived from fresh frozen tumour biopsies which have been subject to multiregional sampling. We will use de novo and reference-guided assembly approaches to generate personal diploid reference genomes and exhaustively explore intratumour genetic heterogeneity. Allele-specific DNA methylation, chromatin accessibility and expression signals from both long and short single-cell reads will highlight how the genetic heterogeneity underpins functional changes. Taken together, this project will contribute to a wholistic, functional understanding of multi-omics variation during somatic evolution. This will uncover novel aspects of cell biology and benefit patients not just with cancer, but with genetic diseases from Mendelian to complex disorders.