Dna Damage REsponse: Actionabilities, Maps and Mechanisms

Project Information

DDREAMM

Grant agreement ID: 855741

DOI

10.3030/855741

EC signature date 16 December 2019

Start date 1 March 2020

End date 31 July 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 8 865 965,00

EU contribution

€ 8 865 965,00

Coordinated by

EIDGENOESSISCHE TECHNISCHE HOCHSCHULE ZUERICH
Switzerland

Periodic Reporting for period 3 - DDREAMM (Dna Damage REsponse: Actionabilities, Maps and Mechanisms)

Reporting period: 2023-03-01 to 2024-08-31

Summary of the context and overall objectives of the project

The DNA of all cells is constantly damaged by environmental factors and internally arising chemicals. To counter this, multicellular organisms have evolved sophisticated mechanisms – collectively termed the DNA-damage response (DDR) – to detect DNA lesions, signal their presence, and promote their repair. While DNA repair pathways have recently been exploited to treat certain cancers, DDR mechanisms are not fully understood and much potential for medical applications for this remains to be explored. DNA repair pathways have also recently been harnessed for “genome editing”, with the potential to yield cures for debilitating genetic disorders. But understanding of how to control genome editing through controlling the DDR is still in its infancy.

The EU-funded DDREAMM project is investigating DDR pathways to identify factors that confer sensitivity or resistance to DNA-damaging agents, and to control genome editing. This project is leading to insights into human genome surveillance, is generating tools allowing precise control of DNA repair and genome editing, and will nurture the development of new therapies for cancer and other diseases.

DNA-damaging agents such as ionizing radiation and chemotherapeutic drugs have long been used to treat cancers. More recently, genome editing agents, such as CRISPR-Cas, are being explored as ways to treat genetic disorders and create cell therapies. While recent advances leading to targeted DDR therapeutics and genome editing reagents, there are still few options and a great deal left unknown. This project will lead to a better understanding of DNA repair and genome editing, and may identify novel therapeutic strategies.

Our overall objective is to develop and understand comprehensive maps of cellular DDR pathway interactions in different cell types. Our focus is on 1) selective differences between cancer cells and normal cells, and 2) interactions between genome editors and DDR in normal cells. Genetic differences between cancer and normal cells could identify opportunities for therapeutic exploitation, while our findings genome editors could yield new approaches to treat genetic disorders. To achieve our goals, we are using an interdisciplinary set of genetic, physical, and mechanistic experiments.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have developed several important computational pipelines: identifying the most frequent mutations in DDR genes from large datasets of patient samples, a user-friendly and scalable interface to integrate and interrogate many genetic screens, and predictive models of interactions between mutations observed in cancer cells and perturbations of DDR genes. These pipelines have produced several new insights and formed an important backbone for ongoing and future experiments.

We have performed a considerable number of genetic screens, searching for interactions between DDR genes and external perturbations. This includes sensitivity and resistance to DNA-damaging chemotherapeutics, interactions between commonly mutated DDR genes and a larger set of DDR-focused perturbations, and large-scale interrogation of interactions between whole pathways. Meta-analysis of these discovery-focused efforts has led to many new hypotheses that have led to ongoing experiments and concrete outputs. Our work reveals fundamental insights into genome maintenance processes and our dataset provides a springboard for mechanistic investigations into connections between DDR factors and suggests multiple interactions that could be exploited in cancer therapy. For example, we have already found several new interactions, for instance between an unusual DNA repair polymerase and a gene often mutated in cancers. And our work has also led to major improvements in the use of a cutting-edge form of genome editing.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Individual and meta-analysis of the genetic screens mentioned above have led to many new hypotheses that are powering ongoing experiments. These will be the major focus for the remainder of the project. We have generated an adaptable and user-friendly computational platform that allows interrogation of, and comparisons between, existing CRISPR genetic-screen datasets. This will be further adapted, broadened and refined as the project continues.

We will be exploring how modulation of certain DDR genes may lead to more effective and more reproducible CRISPR screens, including CRISPR base editing screens. We have already identified a new player in the DDR, and ensuing studies will define how it functions.

We have identified several new candidate DDR proteins and, after validating these, we will explore their mechanisms-of-action and potential relevance to cancer and other diseases. Large scale interaction screens from multiple labs have begun placing these proteins and other poorly annotated factors into pathways and suggesting modes of action.

The findings from our work have revealed cancer-associated mutations that more prominently affect cellular responses to DNA damage and help us understand the underlying molecular mechanisms as well their effect on DNA repair. This may be particularly useful in the clinic, as it could help stratify patients that carry these mutations for specific drugs.