Shendure, Jay AYang, Wei2025-08-012025-08-012025Yang_washington_0250E_28317.pdfhttps://hdl.handle.net/1773/53658Thesis (Ph.D.)--University of Washington, 2025Throughout life, every individual undergoes a wide array of experiences, yet one constant remains: the passage of time across distinct life stages. In the prenatal phase, we develop from a single-celled zygote into a complex embryo through highly orchestrated cell fate decisions. After birth, our bodies continue to grow and learn, eventually entering a phase of gradual decline marked by aging. This aging process is characterized by increasingly disordered changes in cellular states, ultimately leading to dysfunction and cell death. While development and aging are often seen as opposite ends of the life spectrum, they share core biological principles: both involve dynamic gene expression programs, shifts in cellular identity, and remodeling of tissue architecture. A central question in both fields is: what genetic programs govern these transitions in cell states?Despite significant progress, a systematic, single-cell resolution understanding of these genetic programs remains lacking. Two major challenges hinder such efforts: first, it is difficult to obtain continuous human data over time; second, sample conditions are often limited, restricting our ability to assess contributing factors to variation. However, advances in single-cell RNA sequencing (scRNA-seq) now allow us to profile millions of cells across finely resolved time courses. I hypothesize that applying scRNA-seq to in vitro models or closely-related model organisms offers a powerful approach to uncovering the temporal progression of cellular states. In this thesis, I present two projects that leverage scRNA-seq and computational analysis to address this question. In the first project, we used scRNA-seq to study lineage specification in an in vitro model of early human embryogenesis known as gastruloids. We identified a retinoic acid signaling axis that is critical to early embryogenesis and improved the alignment between the in vitro model and the human embryo. Ultimately, we demonstrated that this new enhanced model can be used to study genetic variation during early embryogenesis through large-scale perturbation experiments. In the second project, we performed scRNA-seq on brain samples from rhesus macaques across the lifespan—from early infancy (5 months) to late adulthood (21 years). Through computational analysis, we constructed aging trajectories that capture changes in cell abundance and transcriptional profiles at single-cell resolution. These trajectories allowed us to identify cell subtypes vulnerable to aging and uncover gene regulatory networks driving their transitions. By aligning macaque aging trajectories to human neurodegenerative disease signatures, we observed strong convergence between the two processes. Together, these studies examine the temporal dynamics of gene regulation during both embryogenesis and aging. By establishing a new in vitro platform to model early human development and constructing aging trajectories in the non-human primate brain, we aim to uncover the genetic drivers of cell state transitions across the human lifespan. This work lays the groundwork for a deeper understanding of developmental and aging processes and enables comparative analyses between them.application/pdfen-USnoneGeneticsGeneticsThesis