Single-cell transcriptome analysis of avian neural crest migration reveals signatures of invasion and molecular transitions [scRNA-seq]

Neural crest cells migrate throughout the embryo, but how cells move in a directed and collective manner has remained unclear. Here, we perform the first single-cell transcriptome analysis of cranial neural crest cell migration at three progressive stages in chick and identify and establish hierarchical relationships between cell position and time-specific transcriptional signatures. We determine a novel transcriptional signature of the most invasive neural crest Trailblazer cells that is consistent during migration and enriched for approximately 900 genes. Knockdown of several Trailblazer genes shows significant but modest changes to total distance migrated. However, in vivo expression analysis by RNAscope and immunohistochemistry reveals some salt and pepper patterns that include strong individual Trailblazer gene expression in cells within other subregions of the migratory stream. These data provide new insights into the molecular diversity and dynamics within a neural crest cell migratory stream that underlie complex directed and collective cell behaviors. 501 single cells analyzed from various parts of the migrating neural crest during various timepoints in development. 96 cells from HH11 Trailblazers, 50 cells from HH13 Trailblazers, 50 cells from HH13 Leaders, 60 cells from HH13 Trailers, 50 each from HH15 Trailblazers, Leaders, and Trailers. For definitions, see the extract protocol. Neural crest from a neural tube placed in culture were also analyzed.