Project Summary The genetic causes of human diseases are rapidly being identified thanks to a revolution in human genomics. Progress toward a deeper understanding, however, requires further analysis of the underlying developmental, cellular and molecular mechanisms, as well as the establishment of predictive disease models to test therapeutic options. Ultimately, genes do not function in isolation; they are grouped spatially and temporally at multiple nested levels, the most salient functional unit being the single cell. Observing biological systems at the cellular level provides an unprecedented opportunity to define functional modularity and combinatorial interactions of genes in various physiological contexts. Many of these contexts are conserved in evolution, deviations from which produce important innovations but which also lead to malformations and disease. Accordingly, a Human Cell Atlas is being built with the hope that it will form a core of this single-cell perspective. Parallel work in model organisms will be crucial, and cell atlases are being constructed currently e.g. in mouse and zebrafish. From Gurdon’s discovery of nuclear reprogramming, through characterization of the cyclins that drive the cell cycle, to many recent discoveries on signaling among cells, Xenopus remains at the forefront of biomedical research, as a unique model. We propose to establish a Single Cell Atlas for this important model system which would enhance the value of the unique methods already available in Xenopus and allow effective communication to other experimental systems including human. It will be a critical complement to other emerging Xenopus tools, such as CRISPR-edited mutant lines, which could be most easily characterized in developmental and adult function at the single- cell level. Moreover, the large cell size of amphibian embryonic cells has already made single-cell proteomics possible in Xenopus, well ahead of other organisms; thus, Xenopus is the natural choice for spearheading the shift towards single-cell proteomics. Overall, this project will enhance a critical animal model for the investigation of human disease mechanisms and open new horizons for many already supported NIH projects in other Institutes that focus on specific organ systems and disease.

Project Narrative Due to its unique advantages as an experimental system, Xenopus has for many years revealed key insights into multiple domains of biomedical science including cell biology, embryology, neurobiology, physiology and signal transduction. This proposal seeks to characterize Xenopus at the very deep level of single cell RNA expression in embryonic development through to adult organs, so that it may serve as a better model for the causes and therapies for human disease.