How cancer telomere lengthening pathways shape chromosomal instability and tumour evolution

Primary supervisor: Sarah McClelland, Queen Mary University of London

Secondary supervisor: Simon Boulton, Francis Crick Institute

Project

Chromosomal instability drives tumour genome evolution. Understanding and exploiting vulnerabilities associated with intrinsic and cancer-specific genomic instability pathways provides an opportunity to design new therapies. However, detecting and exploiting specific chromosomal instability pathways in cancer is a long-standing challenge.

Telomeres are repetitive DNA sequences that protect the ends of the chromosomes. In somatic cells telomeres shorten with each cell cycle, ultimately leading to cellular senescence and cell death. Cancer cells must prevent the shortening of telomeres to achieve immortality, and most cancers achieve this by overexpressing telomerase to artificially lengthen telomeres. In 10-15% of cancers, however, cells utilise a different mechanism known as Alternative Lengthening of Telomeres (ALT) [1].

ALT hijacks cellular machinery for genome stability maintenance processes such as homologous recombination and break-induced replication, and the process of ALT appears to create specific types of genomic instability, such as telomere-driven chromosome rearrangements and accidental incorporation of telomere sequences in non-telomeric regions of chromosomes [2]. Importantly, these telomeric sequence insertions – interstitial telomeric sequences (ITSs) – have been suggested to promote chromosomal instability (CIN) as telomeric sequences are difficult to replicate and might generate multiple new fragile sites in the genomes of ALT+ cells. However, this has not been directly tested, nor is the impact on cancer genome evolution known.

ALT is highly common in subsets of aggressive cancers with poor prognosis and without effective therapeutic strategies, particularly in cancers of mesenchymal origin such as sarcomas, and particularly in paediatric osteosarcomas [3]. Therefore, our team is interested in understanding if there are vulnerabilities associated with ALT that could be exploited not only to understand the principles of cancer genome evolution in these tumours, but also to develop new therapies.

This project will use a unique panel of ALT+ cancer cell lines and cutting-edge single cell and single molecule genomic assays to interrogate the types of chromosomal instability caused by ALT. We will track cancer genome evolution over each cell cycle using imaging and single cell genome sequencing [4]. We will examine how DNA replication is impacted by ALT, and by interstitial telomeric sequences using a new long-read sequencing method that maps DNA replication dynamics to specific genomic loci [5]. We will develop methods to track the location of interstitial telomeric sequences in individual cells using CRISPR-Cas9 and single cell sequencing, enabling us to track the kinetics of this process. Discoveries made using experimental models will be mapped on to clinical genome sequencing information from ALT+ tumours.

The unique combination of these approaches on ALT+ cancer genomes will allow not only for deeper understanding of how ALT+ cancer genomes evolve but also contribute to ALT+ cancer stratification and utility of developing targeted therapies for ALT+ cancers.

Candidate background

The candidate will have an interest in genomics and cancer evolution, as well as an interest in translational biology. The candidate may also have cell culture experience and computational skills, however this project is well supported by computational biologists in the McClelland lab, and by core facilities in both supervisor institutes.

Potential placements

1. Simon Boulton, Francis Crick Institute
2. Susana Godinho, Barts Cancer Institute, Queen Mary University of London
3. Simone Zaccaria, Cancer Institute, UCL

References

1. O’Sullivan, R. J. & Greenberg, R. A. Mechanisms of Alternative Lengthening of Telomeres. Cold Spring Harb. Perspect. Biol. 17, a041690 (2025).
2. Sieverling, L. et al. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat. Commun. 11, 733 (2020).
3. Burrow, T. A. et al. Prevalence of alternative lengthening of telomeres in pediatric sarcomas determined by the telomeric DNA C-circle assay. Front. Oncol. 14, 1399442 (2024).
4. Guscott, M. A. et al. Tracking Genome Evolution in Single Cell Clones Reveals the Rates and Features of Copy Number Alterations Generated by Ongoing Chromosomal Instability in Cancer. http://biorxiv.org/lookup/doi/10.1101/2023.09.27.559836 (2023) doi:10.1101/2023.09.27.559836.
5. Jones, M. J. K. et al. A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells. 2022.09.22.509021 Preprint at https://doi.org/10.1101/2022.09.22.509021 (2022).