Development of bulk tumour deconvolution methods:
I have implemented an algorithm to split bulk tumour gene expression into their separate contributions from the underlying normal and cancer cells. This innovation has sparked an ongoing collaboration with the lab of dr. Mansour (UCL Cancer Institute, London, UK) to identify novel cancer genes in acute leukaemia and with the lab of dr. Murchison (Department of Veterinary Medicine, University of Cambridge, UK) to study tumour-host interactions and immune escape in transmissible cancers of dogs and Tasmanian devils.
Together with my PhD student Elizabeth Larose-Cadieux, I have also developed a method to deconvolute bulk tumour DNA methylation data, an important factor in gene regulation. Our method is the first to accurately detect specific genetic variants in this type of data and quantify their allele frequencies to derive the amount of contaminating normal cells and the number of chromosome copies in the cancer cells. In the final step, these confounders are corrected for, yielding the pure tumour methylation profile.
Analysis of single-cell sequencing data:
Single-cell micro-metastases of tumours often occur in the bone marrow. These disseminated tumour cells (DTCs) can lay undetected and dormant for many years, often resisting therapy, before re-activating and giving rise to a new tumour. The nature of DTCs remains elusive, as well as when and from where in the tumour they originate.
In collaboration with scientists in Norway, Belgium, the US and the UK, we sequenced the genomes of 63 single cells isolated from bone marrow donated by six patients diagnosed with localised breast cancer. Comparing the genetic changes in these cells with those identified in the deconvoluted primary tumours we could reconstruct the order of mutations during tumour evolution. In turn this allowed us to trace the origins of the DTC to subpopulations of cancer cells in the primary tumour.
Application to large pan-cancer cohorts – Homozygous deletions and tumour suppressors
Normal human cells have two copies of all genes. Some of these genes are so-called tumour suppressors that can stop cancer developing. Only when both copies of a tumour suppressor are gone – known as a homozygous deletion – do cells progress to cancer. However distinguishing whether a tumour has lost a single or both copies is difficult when samples contain an unknown fraction of normal cells.
We therefore deconvoluted the genomic data of more than 2,200 tumour samples, determining the fraction of normal cells and the number of copies of each gene in the cancer cells. The analysis revealed 96 regions of the genome that are frequently lost during tumour development (see Figure). While some of these are prone to DNA breakage without contributing to tumour development, others contained tumour suppressor genes. Developing a statistical model that uses the footprint of the DNA losses to distinguish between the two, we confirmed 16 established tumour suppressors and proposed 27 previously unknown ones.
Application to large pan-cancer cohorts – Clustered mutational processes
Some processes can generate multiple, typically clustered mutations in a single catastrophic event, leading to substantial reconfiguration of the cancer genome. Three such processes have been described: (i) chromothripsis, in which one or a few chromosomes are shattered and the resulting fragments are stitched together at random; (ii) chromoplexy, in which repair of co-occurring DNA breaks, typically on different chromosomes, results in shuffled chains of rearrangements; and (iii) kataegis, a hypermutation process leading to clustered single base changes on a single DNA strand. We characterised and timed these three processes in the massive Pan-Cancer Analysis of Whole Genomes dataset of 2,658 cancer whole genome sequences.
We found kataegis to be widespread, affecting over 60% of tumours. It appears to activate late during tumour evolution and comes in different flavours, each with specific DNA base changes. While chromoplexy was known to play an important role in prostate cancer, we find it contributes to the development of thyroid cancers as well. Finally, chromothripsis also seems to have different types and is more widespread than previously appreciated. It is an early event in various cancers, most surprisingly melanoma, where it simultaneously disrupts multiple cancer genes.
