Periodic Reporting for period 1 - DeCoDe Platy (Reconstructing the complete developmental lineage of Platynereis dumerilii)
Reporting period: 2021-07-01 to 2023-06-30
Despite their differences in shape, size, and function, all the cells in an animal share the same genome and are created from the same fertilised egg. This incredible diversity of cell types is orchestrated by a complex regulatory apparatus, which guides cell populations towards different fates as development progresses. The mechanisms which change and maintain cell type identity are fundamental for multicellular organisms, shared between species to a remarkable degree, and often dysregulated in ageing or disease.
In this project we studied the early development of a marine worm in order to document how cell types emerge and understand the mechanisms that control cellular differentiation. We gathered snapshots of gene expression with single-cell resolution for various time points during development and tried to stitch them together. We intended to supplement this with data of different types that would provide more context, such as the location of the cell types in the body of the developing worm or the characteristic morphology of each cell type.
Shortly before the mid-point of the fellowship, the fellow received an offer for a permanent position elsewhere. Considering the precarity of employment in research and higher education the fellow felt compelled to accept the offer, and had to give up the fellowship as a result. Both the fellow and the host remain committed to finishing the project despite the formal interruption of the fellowship, and data acquisition has already restarted in the host lab.
In this project we studied the early development of a marine worm in order to document how cell types emerge and understand the mechanisms that control cellular differentiation. We gathered snapshots of gene expression with single-cell resolution for various time points during development and tried to stitch them together. We intended to supplement this with data of different types that would provide more context, such as the location of the cell types in the body of the developing worm or the characteristic morphology of each cell type.
Shortly before the mid-point of the fellowship, the fellow received an offer for a permanent position elsewhere. Considering the precarity of employment in research and higher education the fellow felt compelled to accept the offer, and had to give up the fellowship as a result. Both the fellow and the host remain committed to finishing the project despite the formal interruption of the fellowship, and data acquisition has already restarted in the host lab.
Single-cell (and single-nuclei) RNA-sequencing data was generated for various developmental time points. For certain stages (48 hours post fertilisation, 6 days post fertilisation) we think we are able to identify cell types represented by as few as a handful of cells in an animal; this level of detail is not yet present at other stages. A computational pipeline for the in-silico developmental lineage of Platynereis dumerilii was developed and will be applied when all data has been collected. In the duration of the project I contributed towards improvements in the Platynereis genome, including e.g. the functional annotation of genes, identification of putative transcription factors.
While most dissemination activities were planned towards the end of the fellowship, I had opportunities to present the project to peers and the broader public. I gave regular presentations to my host lab and the department, obtaining corrective feedback. I communicated the project informally during the Platynereis community meeting and the 5th International Congress on Invertebrate Morphology (ICIM5), leading to the formation of new collaborations. Finally, in collaboration with EMBL’s Science Education team, I presented my work to high school students in an effort to debunk stereotypes about research in the life sciences.
While most dissemination activities were planned towards the end of the fellowship, I had opportunities to present the project to peers and the broader public. I gave regular presentations to my host lab and the department, obtaining corrective feedback. I communicated the project informally during the Platynereis community meeting and the 5th International Congress on Invertebrate Morphology (ICIM5), leading to the formation of new collaborations. Finally, in collaboration with EMBL’s Science Education team, I presented my work to high school students in an effort to debunk stereotypes about research in the life sciences.
When the project is completed, it will be one of the few instances where we can follow gene expression during the complete development of an animal. With the additional context provided by the supplementing data we hope to dissect the corresponding regulatory apparatus. This will be a step towards understanding the control mechanisms that govern cell fate and cellular differentiation; these mechanisms are often dysregulated in disease and ageing.