A 3D zebrafish microanatomical and gene expression atlas for disease modeling

Project Summary The zebrafish is a vertebrate model organism with significant genetic, cellular, and physiological similarities with humans. Its powerful genetic and imaging tools have allowed us to decipher gene function, embryonic development, and disease mechanisms. Its small size and recent advances in imaging allow the unbiased visualization of phenotypes across all cell types and tissues through adulthood. This creates a unique opportunity for an integrative atlas resource that will allow the interpretation of multi-omic data in the context of the whole organism. The labeled 3D whole-animal lifespan atlas will be based on microCT customized for histopathology, histotomography that will, in turn, anchor 2D histological and developmental gene expression data to facilitate understanding of normal and abnormal phenotypes. Histology, the study of the microscopic structure of tissues, provides critical understanding of the organization and function of tissue structure across organ systems. Clinical phenotypes are associated with altered gene expression in specific cell types. Single-cell transcriptomic data are best interpreted in the context of the microanatomy of the whole animal. Zebrafish is ideal for testing these principles based on the ability to image the entire organism in 3D at cellular resolution. The integrative zebrafish 3D microanatomical atlas will provide facile access to the first gene expression data anchored on whole-organism, developmental stages, at subcellular resolution. Atlas integration will involve a multi-disciplinary team of researchers with expertise in various fields, including histology, microscopy, imaging, and genomics, and in interdisciplinary research. To ensure the accuracy and completeness of the atlas, we will consult with experts in the field and incorporate feedback from the scientific community. The 2D histology component of the atlases will include vector-based annotation of histology and histology like virtual slices from 3D high-resolution images of the organisms' cells, tissues, and organs. The 3D micro-CT component will consist of cell-resolution 3D reconstructions of key structures, allowing researchers to interrogate spatial relationships between different structures and to manipulate and explore the anatomy of the model organisms in virtual environments. The gene expression component will involve generating both 2D spatial transcriptomic gene expression data (2D spRNA-seq) and single-cell RNA-seq data for a zebrafish, integrating the two datasets to assign cell types likely to be present in each 2D spRNA-seq spot, and performing in situ hybridization experiments to validate the assignment of clusters in three dimensions. A primary goal of this project is to maximize the impact of open-access multimodal, submicron resolution atlasing by facilitating the dissemination of that knowledge across the scientific community. This atlas will comprise a foundation for the long-term goal of applying this approach across model systems and humans that will, in turn, accelerate a broad range of model organism research dedicated to the enhancement of human health.