CNIO researchers create the “human repairome”, a catalogue of DNA “scars” that will help define personalized cancer treatments

(Press-News.org) The human repairome, REPAIRome, will allow researchers around the world to rapidly check out how each of the 20,000 human genes affects DNA repair. Created by researchers at the Spanish National Cancer Research Centre (CNIO), it is published today in the journal Science. The human repairome is ‘a powerful resource for the scientific community’, the authors write in Science. It has ‘implications for human health, including cancer treatment’. It also allows progress ‘towards full control of CRISPR-Cas gene-editing technologies’, they add. The repairome is ‘a platform for new discoveries,’ says CNIO researcher Felipe Cortés. It has already helped to detect new genetic mechanisms involved in kidney cancer. You can always be judged by your scars. This is the idea that sums up one of the new breakthroughs in basic and biomedical research published today in the journal Science, an achievement of the Spanish National Cancer Research Centre (CNIO). It is the “human REPAIRome” – a name that refers to the repair of breaks in the DNA molecule.

A research group at the CNIO has identified the 20,000 types of scars that remain in repaired human DNA after a break. They have subsequently organised them on a website, the human REPAIRome portal, available to the global scientific community. The human repairome is thus the catalogue of scar patterns in repaired human DNA.

This information is valuable as basic knowledge, but also from a medical perspective. For example, being able to interpret the pattern of scarring in a patient's tumour cells can help determine the best treatment for each cancer type.

‘It is an ambitious piece of work, which we hope will become a truly useful resource in cancer research and also in clinical practice,’ says Felipe Cortés, head of the CNIO's DNA Topology and DNA Breaks group and lead author of the paper.

For Ernesto López, one of the first authors of the study, ‘it has been an strenous and painstaking effort because there are some 20,000 patterns, as many as there are genes in human DNA’.

Repairs that leave their mark

DNA is in all our cells and is the molecule from which genes are made, the molecular instructions guiding how the body works. But DNA keeps on breaking, due to the cell's own dynamics and often for such ordinary reasons as exposure to the sun. These injuries are dangerous, and the cell must repair them to survive.

Repairs, however, leave a trace. Each repair leaves behind a trail of genetic alterations, of mutations. Researchers speak of a ‘mutational footprint’ or, metaphorically, the scars left behind after repair.

Decoding scars in repaired DNA may lead to new treatments

These traces contain highly coveted information. Just as the marks on the skin are different after a cut and a burn, the alterations in DNA after a repair reveal the type of damage suffered.

They also reveal other details about, for example, how the cell has repaired the break. In skin, the scar tells the trained eye the stitch used; in DNA, the mutational fingerprint tells what repair mechanisms the cell has used.

So decoding the scar to understand the original damage, and its repair, is important in many areas of research and specifically in cancer. ‘This is very relevant for cancer treatment, because many cancer therapies precisely work by causing DNA breaks,’ explains Cortés.

Cancer treatments often stop working because tumour cells learn to repair the breaks caused by drugs, making tumours resistant to therapy. Understanding how the cell repairs the breaks in each case can help overcome resistance.

20,000 DNA scar patterns

There is one detail that gives meaning to the human repairome: the scar pattern left in a cell's DNA varies depending on which genes are missing or present.

This point is key, because it has made the current breakthrough possible. The CNIO group's achievement has been to reveal how each of our genes affects scarring. The “human repairome” now published in Science contains all possible scarring patterns: it looks at the mutational footprint caused by DNA breaks in 20,000 different cell populations, each of them without a specific gene.

In this way, ‘if you look at certain scars in the DNA of tumours, you can infer which genes are not working, and this is useful for designing specific treatments,’ explains Cortés.

Switching off every one of the 20,000 human genes

The development of the human repairome has therefore required extensive work. CNIO researchers generated some 20,000 different cell populations, disabling (switching off) a different gene in each of them; they then caused breaks in each of them, using the gene-editing tool CRISPR. Finally, they observed the imprint (scar) left on the molecule after the cell repaired the wound.

One of the main advances that made the study possible was to perform this massive analysis simultaneously in all 20,000 populations, rather than one by one. It is a specific technological development that has value in its own right and, ‘can be used for future studies that aim to simultaneously analyse the effect of all human genes,’ says Israel Salguero, co-first author of the study.

Moreover, ‘this has required a significant computational effort, including the development of new analysis and representation tools,’ says Daniel Giménez, researcher in the Chromosome Dynamics group at the CNIO, also co-first author.

For this reason, the CNIO's Computational Oncology and Genomic Integrity and Structural Biology groups have also contributed to this research.

A “scar” associated with kidney cancer

As the authors write in the journal Science, "REPAIRome is a catalogue that shows how each of the about 20,000 human genes affects the patterns of mutations that result from DNA break repair. REPAIRome can provide insights into DNA repair mechanisms, improve gene editing and explain the mutation patterns observed in cancer.”

The REPAIRome web portal will allow researchers around the world to rapidly check out how any human gene affects DNA repair, analyse functional correlations between genes and explore molecular pathways involved. Its authors consider REPAIRome ‘a platform for new discoveries’, adds Cortés.
In fact, the authors publish in Science findings that have already been made possible by REPAIRome. They include new proteins involved in DNA repair, both promoting and preventing it.

They have also discovered a pattern of mutations related both to kidney cancer and to low oxygenation (hypoxia) conditions in other tumours. This is a finding that could lead to new therapeutic approaches in the future.

DNA double helix breaks down

REPAIRome specifically addresses the repair of one of the most serious types of DNA damage, DNA double-strand breaks (DSBs). This is the simultaneous breakage of both strands of the double helix of the DNA molecule, and can be caused by an error during DNA replication or by external factors such as exposure to X-rays, sunlight (UV radiation) or drugs.

Indeed, as mentioned above, cancer chemotherapy and radiotherapy kill tumour cells by causing such ruptures, hence the biomedical importance of understanding how they are repaired - and how to prevent repair. Knowledge of the human repairome may in that sense help to identify new therapeutic targets.

Better control of gene editing

They also hope it will contribute to improving current gene-editing tools, as the new CRISPR-Cas systems are based precisely on inducing breaks to cause specific changes in DNA.

‘In-depth understanding of how double-strand break repair mechanisms operate (...) is an area of extraordinary interest, with implications for human health, including cancer biology and treatment, as well as for our efforts towards full control of CRISPR-Cas gene-editing technologies,’ they write in Science.

The REPAIRome ‘is a powerful resource for the scientific community, and especially for those interested in DSB repair and the biotechnological and medical use of CRISPR-Cas systems,’ they add.

Financing:

This project has been financed with state and European public funds through the joint programme ‘A way of making Europe’ of the Ministry of Science, Innovation and Universities (Spanish Research Agency, AEI) and ERDF funds. Some of the participating researchers have received mainly state funding from the AEI and the Autonomous Community of Madrid, and grants from the “la Caixa” Foundation and the Spanish Association Against Cancer (AECC).

About the Spanish National Cancer Research Centre (CNIO)

The Spanish National Cancer Research Centre (CNIO) is a public research centre under the Ministry of Science, Innovation and Universities. It is the largest cancer research centre in Spain and one of the most important in Europe. It is made up of half a thousand scientists, plus support staff, who work to improve the prevention, diagnosis and treatment of cancer.

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