Periodic Reporting for period 2 - DDREAMM (Dna Damage REsponse: Actionabilities, Maps and Mechanisms)
Okres sprawozdawczy: 2021-09-01 do 2023-02-28
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 a collaboration between three labs (Corn in Zurich, Switzerland; Jackson in Cambridge, UK; and Loizou in Vienna, Austria) 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.
The EU-funded DDREAMM project is a collaboration between three labs (Corn in Zurich, Switzerland; Jackson in Cambridge, UK; and Loizou in Vienna, Austria) 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.
While COVID-related lab shutdowns and supply-chain problems slowed our progress in the first two years, collaborations between the Corn, Jackson, and Loizou labs have already led to several outputs and many more fruitful projects are underway.
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. For example, we have already found several new interactions, for example 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.
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. For example, we have already found several new interactions, for example 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.
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.
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.