Modeling Aneuploidy-Driven Phenotypes Across Tissues - Abstract Aneuploidy, the presence of abnormal chromosome numbers, is a prevalent mosaic genetic anomaly observed at low frequency across all human tissues, with frequency increasing with age. Aneuploidy underlies various human disorders including most forms of cancer, Down syndrome, and miscarriage/infertility. However, relatively little is known about the phenotypic consequences of aneuploidy across different chromosomes and tissues. Over the next five years, our laboratory will address critical knowledge gaps in how aneuploidy alters gene expression and its downstream effects on cellular phenotypes across chromosomes, cell types, and cell states using systems-level, quantitative genetic approaches. Chromosomal copy number alterations (CNAs) impact hundreds or thousands of genes at once, resulting in complex effects within gene regulatory networks (GRNs). We will examine whether CNAs exert phenotypic effects in a cell-type-specific manner, using multiplexed CNA fitness quantification approaches across colon, pancreas, and fallopian tube epithelial cells. These assays will systematically evaluate the fitness impacts of CNAs across the genome, enabling identification of cell-type-specific aneuploidy fitness profiles. This project will leverage human telomerase-immortalized diploid cell models to establish a comprehensive collection of non-lethal aneuploid cell lines from each tissue type, enabling deep investigation into how aneuploidy influences cellular fitness. Additionally, the Watson Lab seeks to better model transcriptomic and phenotypic output of CNAs, since many of the gene expression changes in aneuploid cells affect non-CNA-resident genes. By integrating transcriptomic data with transcription factor regulatory networks, this study will reconstruct tissue-specific GRN models to predict the downstream effects of CNA-driven multigene dosage alterations. These models will be used to explore how CNA-driven signals propagate through regulatory networks, revealing new insights into how CNAs disrupt GRNs to support tumor growth in the case of cancer-enriched CNAs, and, conversely, how GRNs may fail in cases of growth-inhibiting or non-viable CNAs. These studies will thus enhance our understanding of GRN robustness in response to polygenic perturbations. Genome-wide CRISPR screens will be performed to identify essential genes in the context of aneuploidy, with a focus on uncovering synthetic lethal interactions that could be leveraged for aneuploidy-targeting therapies. This comprehensive, systems- level approach will provide unprecedented insights into the mechanisms through which aneuploidy affects gene expression, cellular phenotypes, and disease progression across different tissues.
