Branching across organs: Spatial Mapping of the Developing Mammalian Lung and Submandibular Salivary Gland

Abstract

Branching morphogenesis is a key process during embryonic development that shapes epithelial tubes into the tree-like architectures observed in mature organs, including the airways of the lung and ducts of the salivary gland. Although both organs contain trees of epithelial tubes that form via a similar branching process, it remains unclear whether their development is regulated by common or divergent mechanisms. Exploring the similarities and differences may uncover information that could be used to improve overall respiratory and oral health (i.e., treatments for congenital lung diseases and salivary gland disorders). Furthermore, a better understanding of branching morphogenesis could also suggest innovative tissue-engineering approaches to regenerate or replace lung or salivary tissue. To this end, it is important to understand the spatial patterns of gene expression that take place within the developing lung and salivary gland, which can provide a clue to the underlying signaling pathways and patterns of differentiation in each organ. Thus, my project is focused on high-resolution spatial transcriptomic mapping of the murine embryonic lung and submandibular salivary glands (SMGs), specifically focused on exploring patterns of gene expression at branch points during morphogenesis. First, I dissected murine embryonic lungs and SMGs at their respective key branching stages. I immunostained the whole-mount organs for initial structural analysis. Then, I fabricated microfluidic devices and prepared freshly dissected organs for sequencing by embedding whole-mount organs for tissue sectioning, and running the microfluidic device on top of the tissue section to further examine and compare the branching patterns to determine the optimal branching stage for further genomic investigation. I then combined spatial transcriptomics with deterministic barcoding and computational analysis to explore the potential correlation between spatial patterns of gene expression and patterns of differentiation at branch points of the optimal stages. Whole-mount structural analysis hinted at key similarities between E12.5 murine embryonic lung and E14.5 murine embryonic SMG, which was further verified by immunostaining and sectioning of embedded organs. After further genomic investigation, I discovered key similarities and differences to further elucidate the underlying conserved signaling pathways and mechanisms that regulate branching morphogenesis of different branching organs. My project has made strides in uncovering the extent to which branching is regulated by a conserved signaling pathway in the embryonic mammalian lung and SMG.