CeMM: Artificial gene defect reveals target to fight genetic disease

Fanconi anemia (FA), a rare, inherited disease, is caused by defective genes for DNA-repair in the cells of the patient leading to bone marrow failure, developmental abnormalities and increased cancer risk. Using genome-wide genetic approaches, researchers at CeMM systematically screened for the loss of an additional gene that could rescue the disease – and found it. The corresponding protein turned out to be a potential target that could be therapeutically exploited for FA. The study was published in Nature Communications.

Damaged DNA and its complex repair mechanisms is the research focus of the group of Joanna Loizou, Principal Investigator at CeMM, and finding new molecular targets to fight FA is one of their goals. In their latest study, published in Nature Communications (DOI 10.1038/s41467-018-04649-z), the researchers aimed to find additional genes that genetically interact with the diseased FA genes and are essential for the manifestation of the disease, and thereby, if destroyed, restore the ability of the cell to repair DNA crosslinks. The research project was performed in collaboration with scientists from the University of Cambridge, from the Leiden University Medical Center, the University of California, the University of Toronto and the group of Jörg Menche at CeMM.

The scientists, with former post doc of Loizou´s lab Georgia Velimezi and CeMM PhD student Lydia Garcia-Robinson as shared first authors, deployed a novel genetic screen to search for synthetic viable interactions, using a genome-wide loss-of-function approach that uses insertional mutagenesis achieved via a gene-trap approach, on special lines of FA-defective cells that only possess one copy of each gene. With this method, they scored a bulls eye: the researchers found an enzyme that removes ubiquitin, an important regulator of protein activity and half live, to be synthetic viable for FA gene deficiencies.

When the enzyme, called USP48, was artificially destroyed by CRISPR/Cas9, the FA-deficient cells were less sensitive to DNA-damaging compounds and showed an increased clearance of DNA damage. With further molecular analysis of the underlying processes, the researchers were able to show that the inactivation of USP48 in FA-deficient cells even restored a nearly error free repair of the damaged DNA.

Publication

Georgia Velimezi#, Lydia Robinson-Garcia#, Francisco Muñoz-Martínez, Wouter W. Wiegant, Joana Ferreira da Silva, Michel Owusu, Martin Moder, Marc Wiedner, Sara Brin Rosenthal, Kathleen M. Fisch, Jason Moffat, Jörg Menche, Haico Van Attikum, Stephen P. Jackson and Joanna I. Loizou. (#Co-first Author). Map of synthetic rescue interactions for the Fanconi anemia DNA repair 4 pathway identifies USP48. Nature Communications, June 11, 2018. DOI: 10.1038/s41467-018-04649-z.

Funding

The study was funded by the European Molecular Biology Organization (EMBO), the Austrian Science Fund (FWF), the European Commission, the European Research Council (ERC), the National Institutes of Health (NIH), Cancer Research UK, the Wellcome Trust and the Boehringer Ingelheim Fund (BIF).