Discovering synthetic lethal interactions caused by chromosomal deletions

In this project, we aim to identify synthetic lethal genes associated with chromosomal deletions. As a blueprint, we will use chromosome 1p, as the deletion of it is an early event, e.g. in liver cancer. First, in silico data mining will be applied to identify genes of interest. These genes will be subsequently validated using reverse genetic screens. For this, libraries of sgRNAs and/or shRNAs will be generated targeting the identified genes as well as respective controls. After cloning into expression plasmids, these will be lentivirally infected into human cancer cell lines, preferably of the liver, either harboring chromosome 1p deletion or cell lines without 1p deletion. After narrowing down candidate genes, individual gene knockouts will undergo several functional tests comparing their impact, e.g. on proliferation between the knockout cell lines with and without 1p deletion. If these approaches were successful, the next step would be to investigate the impact of their deletion in vivo. By inducing respective chromosomal deletions in tumors coupled with simultaneous depletion of respective candidate genes via RNA interference, that will allow to investigate the consequences on tumor development and maintenance. In summary, these experiments will help to identify synthetic lethal interactions of chromosomal deletions, which are hallmarks of cancer genomes.

Publication History

Article published online:
23 January 2024