1) Novel signal transduction mechanisms that establish and maintain embryonic boundaries mold the embryo at gastrulation. Prior to gastrulation specification programs cells of the embryo to a general fate (i.e. ectoderm, mesoderm, endoderm), with several sub-territories within these germ layers. At gastrulation those territories are further subdivided as morphogenesis is taking place. The goal of this project is to understand how the specification changes occur over this dynamic period in development using sea urchin as a deuterostome model.
2) Specification of primary mesenchyme cells in such a way that they are prepared to execute an epithelial-mesenchymal transition, and then study mechanistically the regulation of that transition. We identified a number of transcription factors that contribute to the EMT. Genome-wide RNA-seq and single cell seq screens identified candidate genes driven by the EMT-transcription factors. Current efforts examine the cell biology of the effectors whose expression is controlled by the EMT transcripton factors.
3) Specification of endoderm necessary for invagination of the archenteron. The blastopore is highly dynamic during invagination of the archenteron in all deuterostomes. This project examines the local signaling and consequential changes in specification that occur as cells approach, roll through the blastopore and emerge in the extending archenteron.
4) The specification of the immune cells. Several types of immune cells are specified downstream of Notch-Delta and of Nodal signaling. This project examines the specification and diversification of those cell types, and the EMTs that occur as these cells differentiate into functional innate immune cells.
5) Identification and localization of maternal factors in the egg. Egg fragment studies showed if the bottom ¼ of the egg is removed, no endomesoderm is specified, removal of the top ¼ of the egg results in absence of anterior neurons. Rescues, by adding back and expressing maternally localized factors rescues some endomesoderm and neural components. Additional factors for screening are being identified through egg fragment RNA-seq libraries.
6) Formation of the mouth and fusion of the stomodaeum with the foregut. The stomodaeum fuses with the foregut to produce the through-gut in all deuterostomes. Mechanistically little is known about how the stomodaeum is specified and even less is known about how the stomodaeum and foregut associate and form the through-gut. Several assays plus time lapse microscopy approaches are being utilized to understand how this process works using the relatively simple development of the sea urchin as a model.
7) Reprogramming of cells. When cells of the embryo are removed, the remaining cells of the embryo somehow detect the loss of cells. In response, a reprogramming process occurs to replace the missing cells. Ongoing efforts are attempting to understand how the remaining cells sense and respond to the missing cells of the embryo.
In each of these projects we use systems biology approaches, plus microscopy, molecular biology, gene perturbation, and a variety of biological assays including single cell transplants to discover how these important developmental mechanisms work. The sea urchin is the model for these studies and the mechanisms are generalizable as all embryos use these or related mechanisms as part of their repertoire for converting a zygote into an animal.