Tales of aneuploidy: Lessons from (individual) chromosome manipulations

Abstract

Aneuploidy, defined as a karyotype aberration that differs from a multiple of the haploid genome, is a prominent feature of cancer. Aneuploidy commonly arises as a result of chromosomal instability (CIN), when chromosomes are mis-segregated during mitosis. Both CIN and aneuploidy have been associated with tumor heterogeneity, drug resistance, and poor patient prognosis. Interestingly, tumors originating from different tissue types display distinct aneuploidy “signatures”, with each tumor type frequently gaining or losing a specific set of chromosomes. Although CIN has been long established as the cause of aneuploidy, it remains unclear whether certain mis-segregation bias exists, in such a way that some chromosomes have a higher mis-segregation propensities than others. Additionally, the karyotype landscape of tumor cells may also be shaped by factors such as the tissue of origin, oncogenic and mutational background of the tumor, and its microenvironment. How these various elements impact karyotype evolution of the tumor is not entirely understood. Finally, the contribution of recurrent aneuploidies in tumor progression and disease maintenance remains understudied, partly due to the technical challenges in modeling specific aneuploidies in human cells.

In this thesis, I tackle some of these above questions in the field. In chapter 2, I analyze the initial aneuploidy landscapes generated immediately after a round of mis-segregation in non-transformed and transformed cells. By combining single cell sequencing, individual chromosome manipulations, and live-cell microscopy, this study reveals that the nuclear positioning of chromosomes in interphase dictates their segregation behavior during mitosis. Chapter 3 (and addendum) describes the development and initial application of a kinesin-based method that allows for acute induction of specific aneuploidies in human cells at will. By leveraging minus-end-directed motor activities of Kinesin14VIb (Kin14VIb) from the land moss Physcomitrella Patens, we induce polar transport of a chromosome of interest during mitosis, resulting in its mis-segregation and aneuploidy after a single cell division. In chapter 4, I review the classic and novel approaches to model and study specific aneuploidies in mammalian systems. In chapter 5, I address the interplay of chromosomal instability and microsatellite instability in cellular adaptation to challenging conditions. I compare how transient CIN induction affects the adaptability of colorectal cancer HCT116 cells to paclitaxel or low nutrient conditions, depending on their mismatch repair status. I find that a recurrent aneuploidy pattern emerges after transient CIN induction in HCT116 and subsequent culture in low serum, illustrating how the karyotype landscape of cancer cells can be shaped by hostile environmental conditions. Finally, I summarize my findings in chapter 6, highlighting the relevance of this work in the context of existing literature, and discuss possible future directions.