Project Summary/Abstract Despite their important role in birth defects and infant mortality, the 3-D and 4-D patterning processes that employ multiple signals to drive embryonic development and morphogenesis are not mechanistically understood. The long-term goal is to obtain a complete molecular description of 4-D pattern formation, using the simple yet relevant sea urchin larval skeleton as a model. The central objective in this application is to define a model that captures how the ectoderm expresses different patterning cues in different regions over space and time using systems biology approaches, to integrate that network with our spatiotemporal patterning cue reception network in the responsive skeletogenic cells, then use that network model to identify the underlying general principles for spatiotemporal deployment of and response to patterning instructions. The main hypothesis is that differential spatiotemporal expression of the set of signals that regulate skeleton formation is the central driver of embryonic pattern formation and is hard-wired into the ectodermal gene regulatory networks that regulate skeletal patterning, while the reception of those cues drives the spatiotemporal diversification of the skeleton-producing PMCs that in turn mediate morphogenesis. The expected outcomes are (i) a validated single-cell level set of interconnected spatiotemporal network models that define the presentation and reception of patterning cues between the relevant tissues and (ii) computational models that capture the overall network and that will allow rigorous analysis of the networks' functions. The research proposed in this application is innovative, in the applicant's opinion, because it utilizes novel analytical approaches and tools developed by the applicant's group, including a novel scRNA-seq data analysis algorithm, a new tool for automated 3-D mapping of skeletogenic cells from confocal image stacks, and polychrome skeletal labeling for post-hoc dynamics analysis. The proposed research is significant because will establish a highly resolved molecular map of a 4-D developmental process for skeletal patterning that will offer insight into the general principles that underlie complex pattern formation. Because of the conservation of many of the relevant patterning cues between sea urchin and human skeletons, this knowledge may ultimately lead to new approaches for the prevention or treatment of skeletal birth defects and new strategies for synthetic biomineral production.

Narrative The proposed research is relevant to public health because by understanding 4-D developmental pattern formation, it seeks to acquire fundamental knowledge about the mechanisms of embryonic development that are driven by conserved signals and that have the potential to enhance human health by identifying new avenues to prevent or treat patterning- based birth defects. By laying these foundations for new strategies to address skeletal birth defects via increasing our understanding of the fundamental signal-dependent pattern formation processes, the goals of the proposed research are relevant to the mission of NIGMS.