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How cells keep their nucleus clean: a fundamental discovery

Scientists at the Research Institute of Molecular Pathology (IMP) in Vienna have developed a CRISPR-Cas9 screening assay that allows to systematically pinpoint regulators of any gene of interest, including cancer-related genes. Using this approach, they discovered how cells transport their clean-up machinery, the proteasome, into the nucleus to maintain protein balance and get rid of unwanted nuclear proteins. The results of this study are now reported in the journal Nature.

At the Research Institute of Molecular Pathology (IMP) in Austria, scientists in the lab of Johannes Zuber are on the hunt. They are searching for cellular switches that could turn off genes associated with cancer. One of their targets is the gene MYC and its associated protein, which is overly expressed in tumour cells and underlies boosts of cell division.

In a healthy cell, MYC is one of the most shortlived proteins: as soon as its work is done, it needs to be destroyed, or it may cause unwanted cell proliferation. Such is the function of the proteasome, a complex of proteins that acts as the clean-up machinery of the cell. Once a protein is no longer used, the proteasome breaks it apart into smaller peptide pieces.

“The healthy functioning of our organs, tissues, and cells relies on the rapid production and turnover of tens of thousands of proteins. Each protein is controlled by ‘gas pedals’ and ‘brake pedals’, and both can be exploited for the development of drugs,” explains Johannes Zuber, senior scientist at the IMP. “The goal of our study was to pinpoint the gas and brake pedals of cancer-related genes such as MYC, and we found a regulator that we hadn’t expected.”

Two PhD students in Zuber’s lab devised a CRISPR-Cas9 screening assay that allows to eliminate, or ‘knock out’ any gene in the genome in a time-controlled manner, and to see if it affects the abundance of MYC. Should a knocked-out gene result in a decrease in MYC, it could represent a potential drug target for cancer.

Because MYC is essential for cancer cells to grow, its regulation is challenging to study. “Deleting essential genes leads to very quick cell death. However, our screening method allows us to initiate the gene knockout at any chosen moment, so that we can study the immediate consequences of this knockout before the cells start dying,” explains Melanie de Almeida, co-first author of the study and a Vienna BioCenter PhD student.

With their innovative method, the team was able to get a comprehensive view of the regulators of MYC. One of these regulators was a protein they had never heard of.

“In every screen we ran, we found a small protein called AKIRIN2 that appeared to be essential for switching off MYC. Without AKIRIN2, cells showed a strong increase in MYC levels, which was very similar to what we saw when we disrupted the proteasome.” says Matthias Hinterndorfer, cofirst author and Vienna BioCenter PhD student. “It was like the first piece of a puzzle that we wanted to solve.”