PROPOSAL SUMMARY/ABSTRACT Establishing proper cell identities and tissue architecture during early embryogenesis is crucial for a successful pregnancy. Coordination of these processes is integral to patterning the mammalian embryos as they increase complexity from the implantation stages. However, how this tight coordination is regulated remains poorly understood. A high rate of mortality seen in human embryos during the first 2-3 weeks post-fertilization is a major cause of early pregnancy loss, yet the essential cellular, molecular, and mechanical changes remain almost entirely uncharacterized. Rather than merely a structural component that provides physical support, recent studies have shown that the extracellular matrix (ECM) has emerging roles in regulating cell fate specification and morphogenesis. My recent work reveals that the embryonic basement membrane (BM), a specialized ECM, plays an essential role in patterning the early post-implantation mammalian embryo. My preliminary results lay the foundation of my proposal to determine how the BM coordinates the collective cell behaviors and facilitates pattern formation at critical developmental stages of early mammalian embryogenesis. We will apply novel technologies, including 4D quantitative imaging and single-cell spatial genomics, combined with in vivo, in vitro, and in silico approaches to test the hypothesis that the BM facilitates embryo patterning through coordinating cell fate specification and tissue morphodynamics. In my first aim, we will comprehensively map the cell behaviors and the morphodynamics of the developing embryos with 3D quantitative imaging and timelapse imaging approaches. We will define the role of the BM through genetic manipulations in stem cell-derived embryo-like models as well as in the natural embryos. In my second aim, we will map the BM organization and apply single-cell spatial transcriptomics approaches to generate in situ fate maps. We will functionally test how the BM regulates cell identities by quantitatively defining gene expression patterns with BM architecture and validate the findings with loss-of-function analyses. Next, we will build mathematical models that integrate cell identities and cell dynamics with the BM mechanics to uncover mechanisms of pattern formation. In my third aim, we will apply the technologies and tools developed in the previous two aims to explore the roles of the BM in shaping the formation of germ layers during gastrulation. Overall, my proposed work will increase our understanding of how extracellular cues facilitate a successful pregnancy and could inspire novel therapeutic approaches to prevent early pregnancy loss. The training provided by this award will allow me to acquire the necessary skills to develop my independent research program to apply a quantitative systems-level approach to uncover the dynamics, functions, and regulations that shape the embryos at critical stages of early pregnancy.