A Complete Cell Atlas and Lineage Tree of The Immortal Flatworm

Researchers reconstructed a comprehensive lineage tree, including 23 cellular differentiation pathways

Planarians such as Schmidtea mediterranea are popular study objects because they are immortal and can completely regrow if cut into pieces. They possess a large number of adult pluripotent stem cells that constantly renew all tissues and cell types. “For understanding how cells differentiate, we need to compare gene expression profiles from cells at various differentiation stages, like the ones we find in planarians,” says Dr. Mireya Plass from the MDC. “We dissociated whole animals and characterized thousands of individual cells by sequencing their messenger RNA transcripts.” The scientists identified 37 different cell types, 23 of them terminally differentiated, as well as numerous stem cells and so-called progenitor cells at several levels of differentiation.

“We then applied a new computational algorithm, PAGA, developed by Dr. Alexander Wolf, and Professor Fabian Theis in Munich, to predict a lineage tree that includes all identified cell types rooted to a single stem cell group,” says Dr. Christine Kocks from the MDC. This prediction was then combined with additional computational and experimental methods to build a robust tree supported by several independent lines of evidence: sequencing of purified stem cells and cells from stem cell-depleted animals; gene expression changes; unsupervised lineage tree prediction from PAGA; and the results from a recently published method, velocyto, that predicts future cell states from mRNA metabolism estimated from precursor and mature transcripts. In addition, the researchers were able to identify gene programs involved in cell differentiation processes along this tree.

Visualization of messenger RNA specifically expressed in specialized epidermis cells (top), brain and nerve cords (middle) and secretory cells (bottom) from planarians. Dark spots on the left correspond to the eyes of the animal.

Credit: © Salah Ayoub, BIMSB/MDC and Jordi Solana, BIMSB/M

The scientists also discovered several new cell types located in the parenchyma of the animals that had been previously overlooked in molecular studies and that play an important role in the regeneration of flatworms. The proportion of these cells is significantly diminished in regenerating animals, suggesting that these cells “fuel” the body remodeling process in planarians.
Additional online and interactive resources are available to the scientific community

Scientists worldwide have immediate access to the new data on flatworm biology as well as the methods used by the team of researchers. “Our work makes it possible to study stems cells and their lineages in multiple animals. It is not only an important resource for the planarian community, but also provides a cookbook for other scientists that want to perform similar studies in other organisms”, says Dr. Jordi Solana, formerly MDC, now Oxford Brookes University. 

Via an interactive app scientists can interrogate the data and look at the changes in gene expression of specific genes during cell differentiation and regeneration. The detailed online tutorial for lineage reconstruction using PAGA and velocyto will provide a guide for future studies. “Single-cell approaches will become an indispensable method for studying developmental and regeneration biology,” concludes Nikolaus Rajewsky.

Contacts and sources: 

Dr. Christine Kocks  / Dr. Annette Tuffs

Max Delbrück Center for Molecular Medicine in the Helmholtz Association.

Citation: Mireya Plass et al. (2018): “Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics,”, Science. Advance Online Publication 19.04.2018, doi:10.1126/scienc.aaq1723
 

Further Information
Website of the Nikolaus Rajewsky lab
Shiny Web App
online tutorial for lineage reconstruction using PAGA and velocyto