Sp 3dpf scRNA-Seq

Identifying the molecular fingerprint of organismal cell types is key for
understanding their function and evolution. Here, we use single cell RNA
sequencing (scRNA-seq) to survey the cell types of the sea urchin early
pluteus larva, representing an important developmental transition from
non-feeding to feeding larva. We identify 21 distinct cell clusters,
representing cells of the digestive, skeletal, immune, and nervous
systems. Further subclustering of these reveal a highly detailed portrait
of cell diversity across the larva, including the identification of
neuronal cell types. We then validate important gene regulatory networks
driving sea urchin development and reveal new domains of activity within
the larval body. Focusing on neurons that co-express Pdx-1 and Brn1/2/4,
we identify an unprecedented number of transcription factors shared by
this population of neurons in sea urchin and vertebrate pancreatic cells.
Using differential expression results from Pdx-1 knockdown experiments, we
reconstruct the Pdx-1-driven gene regulatory network in these cells. We
hypothesize that a similar network was active in an ancestral deuterostome
cell type and then inherited by neuronal and pancreatic developmental
lineages in sea urchins and vertebrates.

确定生物细胞类型的分子指纹（molecular fingerprint）是理解其功能与进化的关键。在此，我们利用单细胞RNA测序（single cell RNA sequencing, scRNA-seq）对海胆早期长腕幼虫的细胞类型进行调查，该阶段代表了从非摄食幼虫向摄食幼虫转变的重要发育过渡。我们鉴定出21个不同的细胞簇，分别对应消化系统、骨骼系统、免疫系统和神经系统的细胞。对这些细胞簇的进一步亚聚类，揭示了幼虫体内细胞多样性的高分辨率图景，其中包括神经元细胞类型的鉴定。随后，我们验证了驱动海胆发育的关键基因调控网络（gene regulatory network），并揭示了幼虫体内新的活性区域。聚焦于共表达Pdx-1与Brn1/2/4的神经元，我们发现海胆中这一类群神经元与脊椎动物胰腺细胞共享数量空前的转录因子（transcription factor）。利用Pdx-1敲低实验的差异表达结果，我们重构了这些细胞中由Pdx-1驱动的基因调控网络。我们推测，类似的网络在祖先后口动物细胞类型中具有活性，并随后被海胆与脊椎动物的神经元及胰腺发育谱系所继承。