Unraveling the Role of Sonic Hedgehog in Mouse Embryogenesis: Insights from Sonic Hedgehog Knockout Single-Cell RNA Sequencing Data

Abstract

Embryogenesis and cell fate specification is a complex process that lays the groundwork for the entire organism. Development is especially difficult to research and understand in mammals due to the internally developing embryos, slow time scales, and high variability in cell fate determination. However, the conserved importance of morphogens and their downstream signaling pathways has made key ideas in development consistent. Morphogen gradients establish gradual cell patterns along axes. Sonic hedgehog is one of the key morphogens in mammalian development that is involved in dorsal-ventral axis patterning, floor plate and neural cell specification, cardiomyocyte specification, and other structures later in development. Much of the developmental biology research has been done through classical lab techniques, but recent breakthroughs in computational biology and single cell RNA sequencing have offered an opportunity to investigate development through a new lens. I analyzed the impact of a sonic hedgehog knockout on mouse development using single cell RNA sequencing. I investigated differences in single cell RNA sequencing data between wildtype and knockout datasets for different time points. I found differences in tissue composition as well as molecular differences. Overall, I found that sonic hedgehog is required for floor plate development and proper neural differentiation, but it functions only on a few cell states and genes.