Unraveling complex organ regeneration through live imaging and molecular profiling approaches

Project Information

reLIVE

Grant agreement ID: 694918

DOI

10.3030/694918

Project closed

EC signature date 13 September 2016

Start date 1 January 2017

End date 31 December 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 571 694,00

EU contribution

€ 2 571 694,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 4 - reLIVE (Unraveling complex organ regeneration through live imaging and molecular profiling approaches)

Reporting period: 2021-07-01 to 2022-12-31

Summary of the context and overall objectives of the project

There is great biological and medical interest in understanding how some animals can regenerate their body after a severe injury, yet the process is still poorly understood. Understanding regeneration requires studying animals that have such regenerative abilities, like flatworms, crustaceans and salamanders. Our team used a small marine crustacean, Parhyale hawaiensis, as an experimental model to study leg regeneration. We focused on the following questions:
1) Discovering the so-called progenitor cells that contribute to re-making the regenerating leg. To identify these, we marked cells using fluorescent proteins and developed methods to track them under the microscope during the entire course of leg regeneration, which lasts approximately one week. This involved optimising microscopic methods and developing computer software that uses deep learning (a form of artificial intelligence) to facilitate the accurate tracking of cells over very long periods.
2) Discovering the cellular composition and microanatomy of Parhyale crustacean legs and testing whether regeneration produces faithful replicas of the original structures. We described at least 15 cell types with distinct molecular signatures and 8 different types of sensory organs on the surface of these legs, which are all regenerated with striking fidelity.
3) Describing how legs respond to injury, activating new sets of genes in different phases of regeneration. We explored parallels in the way different animals regenerate their legs, including distinct phases of wound healing and leg formation, and an active involvement of nerves.
4) Comparing how legs develop in the embryo with how they regenerate in adult stages. We were interested to find out whether these two processes, which generate identical structures, unfold in similar ways, or whether each is driven by distinct mechanisms. We performed these comparisons at two levels: we compared the sequence of activation of genes (transcriptional responses) and the behaviour of cells during the course of leg development (in embryos) and regeneration (in adults). Unexpectedly, we found that embryonic development and regeneration generate the same structure using different routes.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Live imaging approaches: We took advantage of the unique opportunity offered by Parhyale to image regeneration in live animals, genetically marking cells using fluorescent proteins and observing the entire process of leg regeneration at cellular resolution. This involves continuous live imaging over 5-10 days, which we optimised on a dedicated confocal microscope. To efficiently track cells in these long live recordings, we developed new software to enable semi-automated cell tracking, based on artificial intelligence complemented by manual curation. We used these methods to address two questions: to track the progenitor cells that make new cells in the regenerating leg, and to compare the behaviour of epidermal cells (such as cell division, cell movements, cell shape changes, rearrangements of cells relative to their neighbours, cell death) during leg development and regeneration.

Genetic approaches: A significant part of our efforts was dedicated to developing new genetic tools, such as fluorescent markers for labelling different cell types and tools for stably labelling cell lineages. We tried several approaches which were ultimately unsuccessful (including CRE reporters, gene traps and CRISPR-mediated knock ins), and developed alternative strategies to overcome these failures (e.g. live imaging and post-staining using antibodies).

Transcriptional profiling approaches: To characterise the molecular changes that take place during regeneration, we applied transcriptional profiling techniques (RNAseq) on 120 individual leg samples covering the first 6 days of regeneration. To compare the transcriptional dynamics of develpment and regeneration, a similar dataset was obtained during the course of leg development in embryos. In parallel, we established single-cell transcriptional and chromatin profiling approaches, which served to characterise the diversity of cell types present in Parhyale legs, and to identify specific molecular markers (from snRNAseq) and putative regulatory elements (from snATACseq) for each cell type. The latter serve to develop fluorescent markers that will be used to track their regenerative progenitors by live imaging.

Nerve ablation: The nervous system has been implicated in the control of regeneration in several animals and we want to compare its role across different species. We used a pulsed UV laser to ablate the nerves of Parhyale legs and we studied the effects of this leg denervation on regeneration by live imaging. We found that nerves play distinct roles in early stages of wound healing and in later stages associated with cell division and the formation of the new leg.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Our main achievements in this project have been:
1) We established a robust method for live imaging of regeneration at cellular resolution, which encompasses the entire time course of leg regeneration (up to 10 days post amputation).
2) We developed software for semi-automated cell tracking based on interactive deep learning (sparse manual annotation, followed by deep learning, and proofreading); the software is publicly available via github (https://elephant-track.github.io).
3) We established single-cell and bulk transcriptomics approaches in the context of Parhyale leg development and regeneration. The datasets that we generated, including an atlas of cell types and time series of single-limb transcriptional profiles covering 5-6 days of leg development and leg regeneration, are valuable resources for future studies in the field.
4) We demonstrated that regenerated legs are faithful replicas of the original legs they replace. They are indistinguishable in terms of cellular composition, the molecular profiles of constituent cell types, overall morphology, and the detailed microanatomy and function of the external sensory organs.
5) In spite of the high fidelity of regeneration, we showed that the transcriptional dynamics of leg development and regeneration differ, and cannot be aligned in a coherent manner. This suggests that development and regeneration follow different routes to generate the same structure. This is an unexpected and provocative idea which we will continue to explore at the level of gene regulation.
6) We demonstrated that nerves play an essential role in at least two distinct phases of regeneration, in early wound healing and at the onset of cell proliferation and morphogenesis.

Our project studied leg regeneration in this small marine crustacean, Parhyale hawaiensis