Mapping genetic suppression interaction networks in DNA break repair disorders

Project Information

SupDSB

Grant agreement ID: 101066732

DOI

10.3030/101066732

Project closed

EC signature date 1 June 2022

Start date 1 September 2023

End date 31 August 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 211 754,88

Coordinated by

INSTITUT PASTEUR
France

Periodic Reporting for period 1 - SupDSB (Mapping genetic suppression interaction networks in DNA break repair disorders)

Reporting period: 2023-09-01 to 2025-08-31

Summary of the context and overall objectives of the project

Every time a cell divides it must copy its DNA, and during this process the DNA molecule is constantly exposed to damage. The most dangerous form of damage is a "double-strand break", where the DNA is cut clean through. If such breaks are not mended, cells accumulate genetic errors, become unstable and die. To survive, cells rely on specialized repair pathways.
Two proteins, BRCA1 and BRCA2, are central players in one such pathway. When they are missing, healthy cells normally cannot survive. Intriguingly, the very same proteins, when mutated, are associated with tumorigenic potential: people who inherit a faulty BRCA1 or BRCA2 gene face greatly increased risks of breast, ovarian, prostate and pancreatic cancer. So how can cancer cells lose BRCA1 or BRCA2 and still grow aggressively, when healthy cells die without them?
The answer is that cancer cells adapt by acquiring compensatory genetic changes that let them tolerate the loss of BRCA proteins. Until now, most research studies have focused on tumor cells that adapted long ago, making it very hard to identify which changes were actually responsible for survival.
SupDSB set out to catch adaptation to BRCA-loss as it happens. The core idea was to begin with healthy cells, switch off BRCA1 or BRCA2 suddenly, and then search the whole genome for the helper changes that allow cells to survive. Such survival-enabling changes are known as genetic suppressors. The objectives were threefold: first, to build cell systems in which BRCA1 or BRCA2 can be removed within hours and on demand; second, to test every gene in the genome to find those whose loss rescues - or worsens - survival when BRCA1 or BRCA2 is gone; and third, to connect these laboratory findings to real patient data, in order to judge their relevance for diagnosis and treatment.
Results obtained by SupDSB could have implications for precision medicine. Understanding the routes cells follow to survive BRCA loss should help predict who is most at risk, anticipate how tumors become resistant to therapy, and design treatments tailored to each tumor's exact genetic make-up. Because BRCA-related cancers are common and carry a heavy human and economic cost, the potential benefit to society is substantial.

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

The project first created a powerful new laboratory tool: pairs of otherwise identical ("isogenic") healthy cells in which either BRCA1 or BRCA2 can be destroyed rapidly and completely, simply by adding a small molecule. Because the only difference between the two lines is which protein is removed, their behavior can be compared directly, something earlier studies could not achieve.
Using these cells, genome-wide screens were carried out in which every gene was switched off, one at a time, across large cell populations, before BRCA1 or BRCA2 was removed. Cells that then grew better or worse were tracked over time. This revealed hundreds of genetic changes that either improved survival or conversely worsened it.
A striking finding emerged: the survival routes for BRCA1 loss and for BRCA2 loss are largely different. Only a small set of genes mattered in both cases; while most were specific to one protein or the other. Most surprising were genes with opposite effects — losing them helped cells survive without one BRCA protein, yet harmed cells lacking the other.
The clearest example centered on a protein called FANCM, together with its partners RMI1 and RMI2. Removing FANCM was lethal to cells lacking BRCA1, but beneficial to cells lacking BRCA2, thereby constituting a true “mirror effect”.
The project then focused on establishing why. In BRCA2-deficient cells, FANCM travels to the sites where DNA is being copied (called replication forks) and, with its RMI1/2 partners, promotes the degradation of newly made DNA, fueling genetic instability and death. Removing FANCM, or simply breaking its link to RMI1/2, protected these replication forks, restored normal chromosome stability and growth, and made cells more resistant to PARP inhibitors — an important class of drugs used against BRCA-mutated cancers. In BRCA1-deficient cells, by contrast, FANCM was essential for keeping chromosomes intact, which explains its opposite role.
Finally, the findings were tested against human data. In large public datasets of cancer cell lines, FANCM was indeed essential in BRCA1-mutant cancers but not in BRCA2-mutant ones. Most compellingly, in a patient whose BRCA2-mutant breast cancer failed to respond to a PARP inhibitor, a mutation in FANCM that breaks its link to RMI1/2 became progressively more common in the blood as the tumour resisted treatment, as predicted by our laboratory work.

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)

The project advanced the field in three ways. First, it produced an acute adaptation platform that captures the earliest survival strategies of cells losing a vital gene, instead of studying cells that adapted long ago. This is a versatile tool that can be applied well beyond BRCA biology. Second, it identified that BRCA1 and BRCA2, long treated as equivalent in the clinic, in fact place cells in very different states, with distinct vulnerabilities and distinct survival routes. Third, it identified the FANCM–RMI1/2 machinery acts as a switch whose effect flips depending on which BRCA gene is missing, and which governs both cell fitness and response to PARP-inhibitor therapy.
The potential impacts are clinical. The results indicate that BRCA1- and BRCA2-mutated cancers should not be treated as a single category. Notably, they point to FANCM-RMI1/2 as a candidate marker of resistance to PARP inhibitors in BRCA2-mutant tumors. In the longer term, this could improve patient stratification strategies and match therapy to a tumor's precise BRCA-mutation profile, thereby avoiding treatments that are unlikely to work.
Translating these findings will require further steps: validation in patient groups and additional tumour types; development of reliable tests to detect the relevant mutations in patients; and investigation of drugs that target the FANCM–RMI1/2 axis.