ESR9: “Targeting Genome Fragility in Cancer”

KI (N. Crosetto group): Targeting Genome Fragility in Cancer

i. Objective of research: To identify DNA double-strand breaks hotspots in cancer genomes that can be harnessed for anti-cancer therapy.

ii. Current state of the art: DNA double-strand breaks (DSBs) are ubiquitous in cancer cells, where they accumulate as a result of mutations in genes involved in DNA damage response, oncogene-induced DNA replication stress, and deregulated transcriptional processes. DSBs pose a major threat to genome stability, leading to the formation of genomic rearrangements, which in turn can drive tumor progression. Although it is well established that certain genomic regions, known as chromosomal fragile sites, are more prone to break under specific conditions, the genomic landscape of DSBs in different tumor types remains largely uncharted. In relation to this, several fundamental questions need to be answered: What are the factors that dictate the probability of a given genomic locus to break in different tumor types? Are there vulnerable genomic regions where DSBs have a higher probability of triggering cell death? If so, what are the mechanisms that regulate the response to DSBs at distinct genomic locations? Here, we aim to address these questions and identify actionable cancer-specific vulnerable DSB hotspots where the induction of DSBs results in cancer cell death.

iii. Research methodology and approach: In this project, we will 1) identify vulnerable DSB hotspots in well-established cancer cell lines and 2) explore the type of DNA damage response and effects on cell viability of targeted DSB induction inside identified vulnerable hotspots. First, we will apply our recently developed method for high-throughput DSB sequencing, BLISS, aiming to generate high-resolution genome-wide DSB maps in cancer as well as non-cancerous control cell lines selected among those thoroughly characterized in the Encyclopedia of DNA Elements (ENCODE) project. Second, by comparing the obtained DSB maps with genomic rearrangement profiles measured in the corresponding tumor type in The Cancer Genome Atlas (TCGA), we will identify putative vulnerable regions as DSB hotspots where the frequency of genomic rearrangements is unexpectedly low. Lastly, we will use CRISPR technology to induce multiple DSBs inside these putative vulnerable regions as well as in non-fragile control regions, and monitor the resulting DNA damage response and effects on cell viability.

iv. Originality and innovative aspects of the ESR project: This is an unprecedented effort to systematically characterize the genomic landscape of DSBs in well-established cancer cell lines, and a unique approach to discover novel targets for anti-cancer therapy.

v. Integration of the ESR project to the overall research programme: Our ESR will work with the Branzei and the Legube groups to map the genomic landscape of DSBs induced upon knock-out of key replication factors or NER proteins in cancer and NER-defective cells, respectively and with Genevia on ChIP-seq analysis pipelines.