Functional Understanding of Chromosome Arm Aneuploidies

Project Summary Aneuploidy (gain or loss of a chromosome) and partial aneuploidy (gain or loss of a chromosome arm) have long been observed in cancer cells and are the cause of several congenital diseases. Interestingly, advances in next-generation sequencing have more recently demonstrated the presence of aneuploidy in healthy cells. The goal of this research proposal is to uncover the downstream effects of individual aneuploidies. We developed new computational algorithms to identify aneuploidy events from genomic and transcriptomic data. Our methods allow for identification of small populations of aneuploid cells from bulk sequencing data. In addition, single-cell sequencing of healthy tissues will allow for identification of even rarer aneuploidy events. By leveraging existing comprehensive efforts to characterize single cells from across the human body, we will build an atlas of aneuploidy events occurring in healthy tissue. To directly test the effects of aneuploidy alterations in human cells, I developed a genome engineering approach for targeted deletion of chromosome arms in vitro. We previously used this approach to generate isogenic cell line pairs with and without chr3p deletion and found that chr3p deletion leads to cell cycle arrest. Some of our cell lines adapted to chr3p deletion by duplicating their wildtype copy of chr3, transitioning to a state of chr3q gain. Cells with chr3q gain showed differential dependency on genes involved in DNA replication. Here, we will use these cells to identify the mechanisms of these cell cycle phenotypes, as well as determine which chr3 genes contribute to these phenotypes. In addition, we will create a library of cell lines for each chromosome arm deletion. These cell lines will be critical to compare and contrast the downstream effects of different aneuploidy events in human cells. With this work, we will firmly establish a research program dedicated to understanding the consequences of specific aneuploidies in human cells.