Whole transcriptome sequencing of mouse notochord-derived cells at developmental stages E12.5 and P0

Recapitulation of developmental signals represents a promising strategy for treating intervertebral disc degeneration. During development, embryonic notochord-derived cells (NDCs) are the direct progenitors of cells that populate the adult nucleus pulposus (NP) and are an important source of secreted signaling molecules. The objective of this study was to define global gene expression profiles of NDCs at key stages of embryonic disc formation. NDCs were isolated from Shh-cre;ROSA:YFP mice at embryonic day 12.5 and postnatal day 0, representing opposite ends of the notochord to NP transformation. Differences in global mRNA abundance across this developmental window were established using RNA-Seq. Principal component analysis revealed clustering of gene expression at each developmental stage with more than 5000 genes significantly differentially expressed between E12.5 and P0. This study represents the first transcriptome-wide analysis of embryonic NDCs. Results suggest signaling and biosynthesis of NDCs change dramatically as a function of developmental stage. Overall design: For these studies, we used the Shh-cre;ROSA:YFP mouse model, previously established and shown to express YFP in SHH-expressing notochord cells and their progeny at any developmental stage. Animals were euthanized at two developmental stages, embryonic day 12.5 (E12.5) and postnatal day 0 (P0), representing opposite ends of the notochord to NP transformation. Biological replicates (n=4 at both time points) each consisted of pooled embryos or pups (~6) from a single litter.