Periodic Reporting for period 1 - ModEvoCell (Modelling cell type evolution in animals)
Reporting period: 2022-04-01 to 2024-03-31
This project set out to explore the evolutionary dynamics of cell type change in the animal lineage (the Metazoa). Animals are built from an array of specialised cell types and tissues that constitute the physical and functional building blocks of their complex multicellular organisms. These cell types are complex phenotypes controlled by multiple biological phenomena—ontogeny, morphology, regulatory and transcriptional states, etc.—that are encoded by a single genome (that of the animal). Therefore, these phenomena are subject to the evolutionary process and can be studied from a functional genetic point of view — i.e. studying the patterns of conservation and divergence of the various genetic traits that determine cell phenotypes.
I proposed to investigate the evolution of animal cell types in a comparative framework involving multiple species. The study of the cell type and transcriptomic programmes of various species along a spectrum of phylogenetic divergence times allowed me to outline a data-driven model of evolution that quantifies the influence of regulatory divergence on cell type evolution.
As a biological model for this project, I selected multiple placozoan species. Placozoans are microscopic sea-dwelling animals with limited cell type diversity (thus enabling in-depth single-cell transcriptomic analysis at low cost) and highly conserved genomes (thus enabling straightforward and information-rich cross-species comparisons). Thus, they are ideal models for an initial study of cell type evolutionary modelling. In that regard, the three main aims of the project were:
Aim 1 – Catalogue cell types, regulatory regions and gene regulatory networks across placozoans, using single-cell transcriptomics, regulatory profiling (ATAC-seq), and gene module modelling.
Aim 2 – A cross-species comparative analysis of the determinants of cell type identity, using genetic and functional phylogenetic models.
Aim 3 – Build models of cell type and regulatory evolution in placozoans, integrating information from Aims 1 and 2 in a unifying framework.
This project was devised at a time when single-cell transcriptomic atlases from various species are becoming increasingly available. The ensuing deluge of data enables unprecedented large-scale comparisons and could revolutionise our understanding of cell behaviours in a way similar to the advances brought about by the advent of comparative genomics. Understanding how genetic variation relates to cell type innovation and conservation is central to this endeavour, and I thus sought to cover this gap.
I proposed to investigate the evolution of animal cell types in a comparative framework involving multiple species. The study of the cell type and transcriptomic programmes of various species along a spectrum of phylogenetic divergence times allowed me to outline a data-driven model of evolution that quantifies the influence of regulatory divergence on cell type evolution.
As a biological model for this project, I selected multiple placozoan species. Placozoans are microscopic sea-dwelling animals with limited cell type diversity (thus enabling in-depth single-cell transcriptomic analysis at low cost) and highly conserved genomes (thus enabling straightforward and information-rich cross-species comparisons). Thus, they are ideal models for an initial study of cell type evolutionary modelling. In that regard, the three main aims of the project were:
Aim 1 – Catalogue cell types, regulatory regions and gene regulatory networks across placozoans, using single-cell transcriptomics, regulatory profiling (ATAC-seq), and gene module modelling.
Aim 2 – A cross-species comparative analysis of the determinants of cell type identity, using genetic and functional phylogenetic models.
Aim 3 – Build models of cell type and regulatory evolution in placozoans, integrating information from Aims 1 and 2 in a unifying framework.
This project was devised at a time when single-cell transcriptomic atlases from various species are becoming increasingly available. The ensuing deluge of data enables unprecedented large-scale comparisons and could revolutionise our understanding of cell behaviours in a way similar to the advances brought about by the advent of comparative genomics. Understanding how genetic variation relates to cell type innovation and conservation is central to this endeavour, and I thus sought to cover this gap.
Aim 1 (“Catalogue cell types, regulatory regions and gene regulatory networks across placozoans”) was fully fulfilled, albeit with less species than initially planned (four instead of six) due to sampling constraints, selecting four species from three genera (Trichoplax, Hoilungia and Cladtertia) instead. This updated sampling covers the global same spectrum of phylogenetic diversity.
Then, we produced complete whole-organism atlases of cell behaviour using single-cell transcriptomic approaches (~15,000 cells sampled in each of the four species), covering all known cell types and even revealing novel ones. In parallel, we produced a complete catalogue of active regulatory regions using bulk ATAC-seq, which we then linked to cell type-specific genes (obtained from the expression data) to obtain cell type-specific sets of regulatory regions. Finally, gene coexpression patterns at the cellular level were leveraged to group genes into coordinated modules. Using this information, I sought to establish the degree of evolutionary conservation and divergence between the four sampled species (“Aim 2 – A cross-species comparative analysis of the determinants of cell type identity”). All four species possessed the same basic cell types (epidermal, gland-secretory, lipophilic cells, fibre contractile cells, and peptidergic-secretory cells), which could be further subdivided in each of the species into functionally distinct subtypes (particularly the peptidergic ones). Based on patterns of expression similarity of orthologous genes across species, I was able to build a phenetic cell type tree that approximated evolutionary relationships between these cell type expression programmes across hundred of millions of years of evolution. However, attempts to obtain similar results based on regulatory region activity were largely unsuccessful, which indicated that this trait was faster-evolving and thus less likely to reflect the underlying phylogenetic signal (“Aim 3 – Build models of cell type and regulatory evolution in placozoans”). This unexpected result prompted me to quantify the rate of conservation decay of various determinants of cell type identity over evolutionary time, revealing consistent patterns whereby, within each homologous cell type, gene expression was more conserved than regulatory element usage (and, within genes, master transcriptional regulators were more conserved than downstream effector genes). Crucially, I was also able to contrast these patterns with those of genome-level sequence evolution.
Then, we produced complete whole-organism atlases of cell behaviour using single-cell transcriptomic approaches (~15,000 cells sampled in each of the four species), covering all known cell types and even revealing novel ones. In parallel, we produced a complete catalogue of active regulatory regions using bulk ATAC-seq, which we then linked to cell type-specific genes (obtained from the expression data) to obtain cell type-specific sets of regulatory regions. Finally, gene coexpression patterns at the cellular level were leveraged to group genes into coordinated modules. Using this information, I sought to establish the degree of evolutionary conservation and divergence between the four sampled species (“Aim 2 – A cross-species comparative analysis of the determinants of cell type identity”). All four species possessed the same basic cell types (epidermal, gland-secretory, lipophilic cells, fibre contractile cells, and peptidergic-secretory cells), which could be further subdivided in each of the species into functionally distinct subtypes (particularly the peptidergic ones). Based on patterns of expression similarity of orthologous genes across species, I was able to build a phenetic cell type tree that approximated evolutionary relationships between these cell type expression programmes across hundred of millions of years of evolution. However, attempts to obtain similar results based on regulatory region activity were largely unsuccessful, which indicated that this trait was faster-evolving and thus less likely to reflect the underlying phylogenetic signal (“Aim 3 – Build models of cell type and regulatory evolution in placozoans”). This unexpected result prompted me to quantify the rate of conservation decay of various determinants of cell type identity over evolutionary time, revealing consistent patterns whereby, within each homologous cell type, gene expression was more conserved than regulatory element usage (and, within genes, master transcriptional regulators were more conserved than downstream effector genes). Crucially, I was also able to contrast these patterns with those of genome-level sequence evolution.
This project fulfilled its main aims to characterise, dissect and quantify the patterns of conservation/divergence of cell type identity traits across a section of the metazoan tree of life. The selection of a tractable biological model (placozoans) ensured the success of the project and facilitated the generalisation of our findings to more complex models, as well as the ability to explore wider/narrower evolutionary timescales in the future.
In addition, this project provided crucial novel insights into the evolution of the animal nervous system. Among the cell types identified in all sampled placozoan species were peptidergic secretory cells, which our phylogenetic comparative analyses revealed to be strikingly similar to the neurons present in other animals with complex nervous systems. This shed new light onto our understanding of the origin and evolution of the animal nervous system. This finding highlights the enormous potential for fundamental biological ressearch that stems from studying oft-overlooked animal models such as placozoans.
All code, data and methods resulting from this project were made available to the wider community via public-facing repositories and servers:
https://github.com/xgrau/placozoa-cell-type-evolution-code(opens in new window)
https://sebelab.crg.eu/placozoa_cell_atlas/(opens in new window)
In addition, this project provided crucial novel insights into the evolution of the animal nervous system. Among the cell types identified in all sampled placozoan species were peptidergic secretory cells, which our phylogenetic comparative analyses revealed to be strikingly similar to the neurons present in other animals with complex nervous systems. This shed new light onto our understanding of the origin and evolution of the animal nervous system. This finding highlights the enormous potential for fundamental biological ressearch that stems from studying oft-overlooked animal models such as placozoans.
All code, data and methods resulting from this project were made available to the wider community via public-facing repositories and servers:
https://github.com/xgrau/placozoa-cell-type-evolution-code(opens in new window)
https://sebelab.crg.eu/placozoa_cell_atlas/(opens in new window)