Abstract
Aneuploidy is a hallmark of cancer and one of the main causes of miscarriages in humans1. Recent technical developments in the field of genomics allows one to count the number of chromosomes in a single cell at high-throughput. Using our recently developed single-cell karyotype-sequencing (scKaryo-seq) technique, we tried to answer
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three long-standing questions in the field of aneuploidy: 1. Are certain chromoso¬mes more likely to mis-segregate compared to others and if so, how? 2. How do cells respond differently to specific whole chromosome copy number changes? 3. How common is aneuploidy in human embryos? In this thesis, we first introduced the process of mitosis and the causes and consequences of when it goes wrong (Chapter 1). We then reviewed the prevalence, causes and consequences of non-random segregation errors (Chapter 2). In Chapter 3, we found that multiple different mitotic perturbations in various human cell lines led to the non-random mis-segregation of chromosomes. By following the behavior of single chromosomes during mitosis or by altering their location in the nucleus, we determined that peripherally located chromosomes, which are usually relatively large in size, are more likely to undergo segregation errors than centrally located ones. We also find that this happens in several chromosomally unstable cancer cell lines. We hypothesize that peripherally located chromosomes and in particular those ending up behind the spindle poles in mitosis are at higher risk to mis-segregate, because they experience more challenges in acquiring bi-oriented microtubule connections. In Chapter 4, we characterize the LossTag tool. This tool can be used to enrich for cells with specific monosomies, which allowed us to study the evolution of karyotypes of single cells over time and identify monosomy-specific responses. In Chapter 5, we use scKaryo-seq on 5 day old human embryos to show that chromosomal mosaicism is especially prevalent. Not only is it frequent, but we reason it is also commonly missed during bulk-sequencing because aneuploid cells are often present at low levels. In the current Chapter 6, I discuss our findings in the light of other literature and suggest potential research avenues. I propose explanations of why polar chromosomes so frequently mis-segregate compared to non-polar chromosomes, discuss the presence of mis-segregation biases in cancer cells and explore its consequences. Next, I suggest a potential use for the LossTag tool to help explain recurrent aneuploidy patterns. I conclude this section by debating the consequences of our findings in embryos on preimplantation genetic testing of aneuploidy and argue how in the future different single-cell sequencing approaches can help us better understand the pervasiveness of aneuploidy in healthy tissue.
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