Learn from the Errors at the Start of Life: Dissect Cellular Fitness Through Dynamics of Chromosomal Instability in Embryogenesis

Project Summary Chromosomal instability (CIN), characterized by changes in chromosome number and structure, leads to aneuploidy (abnormal chromosome numbers) and copy number variations (CNVs), where specific genomic regions are duplicated or deleted. Although often considered a hallmark of tumor transformation and cancer, CIN is also surprisingly prevalent in human embryos from the first cleavage event. These initial divisions are directed by maternal machinery pre-loaded into oocytes before genome activation, making early embryogenesis particularly prone to errors, resulting in a high prevalence of mosaicism. Some embryos with both normal and aneuploid cells develop to term by selectively eliminating abnormal cells, suggesting robust elimination mechanisms that favor euploid cells through differentiation and selective apoptosis of aneuploid cells. While CIN in cancer has been intensively studied, the mechanisms of CIN progression and tolerance in tumor cells remain poorly understood. This gap is even more pronounced in early development due to ethical and technical challenges in studying human embryos and fetuses, and the lack of suitable model systems to examine chromosomal and cellular phenotypes. The remarkable resilience of embryos to chaotic chromosomal events highlights embryogenesis as a unique platform for understanding cell-type specific and context-dependent cellular fitness. Leveraging stem cell and organoid techniques with state-of-the-art genomic and imaging tools, the proposed study aims to establish a unique, controllable, and easily modulated in vitro model system using the embryonic and extraembryonic stem cell lines we have developed to capture embryogenesis traits and reflect CIN status. The study will address three main questions: 1. Cell type-dependent intrinsic mechanisms of CIN tolerance and suppression reflected in stage-specific stem cell lines will be uncovered through CNV-revealing single-cell multi- omics and modulated through high-throughput genomic tools. 2. Context-dependent cell competition will be dissected to explore modulation strategies targeting specific pathways, including p53, Myc, and Hippo, as well as identified non-canonical cell competition pathways. 3. Non-cell-autonomous environmental cues in the uterus that affect and constrain CIN will be investigated through a unique co-culture system with endometrial organoids. This research opens new avenues for studying cellular fitness in the context of CIN. The information gained will pave the way for therapeutic innovations that harness the body’s own mechanisms to correct chromosomal imbalances, potentially leading to advancements in enhancing embryo viability. Additionally, through these innovative strategies, I aim to develop comprehensive and powerful new methodologies that could be applicable to studying other CIN-affected disease or condition prognosis.