Resolving spinal cord cell type evolution with single cell sequencing

Project Information

ScLamprey

Grant agreement ID: 895927

DOI

10.3030/895927

Project closed

EC signature date 24 March 2020

Start date 1 November 2020

End date 19 April 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 224 933,76

EU contribution

€ 224 933,76

Coordinated by

THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORD
United Kingdom

Periodic Reporting for period 1 - ScLamprey (Resolving spinal cord cell type evolution with single cell sequencing)

Reporting period: 2020-11-01 to 2022-10-31

Summary of the context and overall objectives of the project

The emergence of vertebrates was accompanied by a major increase in nervous system complexity, as a sophisticated brain and spinal cord evolved to process enhanced sensory input and direct co-ordinated motor output. Such complexity is achieved by an increase in cell number, a greater diversity of cell types and sophisticated mechanisms to organise them. Is has long been debated whether the “2R” whole genome duplications (WGD), which occurred just before the vertebrate split, contributed to the vertebrate increased complexity. To address this, we focus on the lamprey spinal cord –a representative of the first branching vertebrates – and relate gene duplication events to the emergence of new neural cell types. Bulk RNA sequencing and developmental studies have started to shed light on neural patterning mechanisms in lamprey, but they do not provide cellular resolution in this complex tissue. This project combines traditional molecular methods with cutting-edge single cell mRNA profiling, to explore (1) the cellular diversity of the lamprey spinal cord, (2) the molecular mechanisms that specify those cell types and (3) the evolutionary origins of these mechanisms.

The action produced a cellular atlas of the lamprey spinal cord and demonstrated that genes duplicated through whole-genome duplication (WGD) events became incorporated into distinct gene regulatory networks (GRNs), contributing to the evolution of vertebrate complexity.

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

First, I identified marker genes that define specific cell types in the lamprey embryonic spinal cord and confirmed their expression with in-situ hybridisation. Second, I identified distinct transcriptional signatures for each lamprey cell type. Finally, I compared the lamprey spinal cord to that of other chordates, and related gene duplication to the evolution of new cell types.

This action generated 6 spinal cord transcriptomes at single cell resolution of three embryonic stages (2 biological replicates). The data will be soon publicly available with an open-access publication including:
- a catalogue of spinal cord cell type markers, which may be particularly useful to future studies on basal vertebrates and chordates nervous system. This includes phylogenetic analyses and microscopy pictures of gene expression patterns that can be readily re-used as a reference by fellow researchers.
- the six scRNAseq datasets, which provide the basis to reconstruct spinal cord neural cell type gene regulatory network in lamprey.
- the conclusions drawn from our comparative study of several chordate scRNAseq datasets, which sheds light on the evolutionary origin of the vertebrate (and thus human) nervous system. This provides the basis to reconstruct regulatory modules that control spinal cord development and that are conserved in chordates, and identify homologous cell types in chordates.

The action and early results were presented at the meeting of the European Evolutionary Developmental Biology (EED) 2022.
The training component of the action was accomplished through a combination of independent learning and participation in courses.

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)

The data is relevant to broader and highly topical fundamental questions regarding both spinal cord biology and cell type evolution. This may also support our understanding of the diseased spinal cord, especially relevant as lamprey can regenerate their spinal cord. Our atlas complements recent single-cell studies and contributes to the community effort to trace the origins of every human cell type. It provides invaluable insights into the evolutionary forces driving the diversification of cell types, particularly the role of the 2R genome duplications in shaping vertebrate evolution.

The data will also provide a reference framework for aligning future non-transcriptomic single-cell lamprey data (e.g. single cell chromatin data). This is being explored in a grant proposal currently under review.

UMAP of lamprey spinal cord cells coloured according to their cell types