Periodic Reporting for period 2 - EvoCELL (Animal evolution from a cell type perspective: multidisciplinary training in single-cell genomics, evo-devo and in science outreach)
Reporting period: 2020-01-01 to 2022-06-30
Throughout the evolution of animals, the cells that compose their bodies have become increasingly diverse; each cell type is distinguished by the unique set of genes it expresses. The processes by which cells acquired such diverse roles remain poorly understood. Currently, we do not even know how many distinct cell types animals possess, how new cell types arise in evolution, how many are in common between different animal groups, and how many unique cell types have evolved in different animal lineages. Composed of a network of 12 laboratories spread across Europe, EvoCELL studied these fundamental questions in animal evolution and development through extensive use of single-cell RNA sequencing (scRNA-seq). EvoCELL’s scientific aim was to characterize and compare different cell types and tissues in a diverse array of vertebrates and invertebrates showing broad phylogenetic coverage. We sampled data from all major animal lineages and developed new tools for data analyses, through which we pioneered three branches of cell evo-devo: the evolution of stem cells; the emergence of animal life cycles, and the diversity of neural cell types. The EvoCELL network also had a strong focus on science communication. We aimed to find new solutions to exhibit highly complex and contemporary science and so successfully developed the virtual exhibition “Life: through the looking glass” which showcases the research of EVOCELL by emphasizing the procedural nature of science. EvoCELL harnessed and expanded European excellence's world-leading expertise in evo-devo and single-cell genomics by training a new generation of multidisciplinary scientists skilled in exploring the vast breadth of animal differentiation. Over the course of 4 years, the EvoCell fellows acquired highly advanced and diverse scientific skills (single-cell biology and paleontology to bioinformatics) that enhanced their career prospects. Also, they were equipped with outreach and many other complementary skills for a variety of future careers across sectors.
One focus of the network has been on the evolution of neurons and nervous systems. Based on extensive scRNA-seq and in situ sequencing data, we established a cell type atlas of the sea lamprey brain. By comparing this dataset to neural data from other vertebrates we revealed an ancestral vertebrate cell type complement. We also looked into the nervous systems of invertebrate species. We used scRNA-seq to unravel the neuronal diversity in sea urchin larva. We found that a subset of the sea urchin neurons show genetic similarities with vertebrate endocrine pancreatic cells, suggesting a common evolutionary origin. For the marine annelid Platynereis, we found that the mushroom bodies have sensory properties and that they resemble the vertebrate telencephalon by molecular anatomy. We have also characterized the ciliomotor neuron type in Platynereis by combining single-cell atlas analysis and functional studies. We explored the diversity of the neuronal populations in cnidarians by looking into a single cell atlas of the Clytia hemisphaerica adult medusa, we found a higher level of differentiated neural cell types than previously described. We have also characterized neuron diversity in the arthropod clade, which was assessed by doing sc-RNAseq in the spider Parasteatoda tepidariorum. We profiled embryos at a developmental stage marked by the beginning of brain differentiation and found nervous system-patterning genes that had never been described in spiders before. Altogether, this pioneering work opens up for exploring the diversification of neurons and nervous systems during evolution.
Another focus has been on regeneration. We examined the fidelity of Parhyale hawaiensis leg regeneration. We found that regenerated legs are precise replicates. Single-nuclei RNA seq showed that regenerated and uninjured legs are indistinguishable in terms of cell type composition. Also, by comparing the global transcriptional dynamics of leg regeneration and development in Parhyale we showed that these two processes show distinct temporal profiles of gene expression. Related to this, we investigated the role of piRNAs and PIWI proteins in stem cell maintenance, differentiation and cancer. We developed a bioinformatics tool to identify and annotate somatic piRNAs and used it to identify the piRNA complement in: sea urchin P. lividus embryos, differentiating cardiomyocytes and in colon-rectal cancer (CRC) cell lines. Also, we have characterized the activity of the PIWI/piRNA pathway in CRC cells and found that it may contribute to the establishment and/or maintenance of clinicopathological features of colon cancer.
In addition, we were interested in the life cycle of marine invertebrates and how the cell type complements change between larval and adult stages. We generated single cell expression atlases of different developmental stages in diverse organisms and defined stage-specific and common cell types. For the planula and medusa stages in Clytia hemisphaerica we found both: cells, with unique transcriptional programs, and cell types with conserved gene expression programs between both stages. We could detect shared elements in the transcriptional signature between neural cells and mature nematocytes, allowing us to propose evolutionary scenarios about their emergence. Also, intending to reconstruct the evolution of the neural and secretory cell types at the aboral end of the cnidarian planula larva, we compared Clytia and the stony coral Pocillopora acuta. Also, we aimed to identify potential homologous cellular lineages in two species of Lophotrochozoan larvae.
The results of our research were published in high-impact peer-reviewed scientific journals and were presented at prestigious international conferences. Also, we organized several outreach activities to disseminate the results of our research to the general public.
Another focus has been on regeneration. We examined the fidelity of Parhyale hawaiensis leg regeneration. We found that regenerated legs are precise replicates. Single-nuclei RNA seq showed that regenerated and uninjured legs are indistinguishable in terms of cell type composition. Also, by comparing the global transcriptional dynamics of leg regeneration and development in Parhyale we showed that these two processes show distinct temporal profiles of gene expression. Related to this, we investigated the role of piRNAs and PIWI proteins in stem cell maintenance, differentiation and cancer. We developed a bioinformatics tool to identify and annotate somatic piRNAs and used it to identify the piRNA complement in: sea urchin P. lividus embryos, differentiating cardiomyocytes and in colon-rectal cancer (CRC) cell lines. Also, we have characterized the activity of the PIWI/piRNA pathway in CRC cells and found that it may contribute to the establishment and/or maintenance of clinicopathological features of colon cancer.
In addition, we were interested in the life cycle of marine invertebrates and how the cell type complements change between larval and adult stages. We generated single cell expression atlases of different developmental stages in diverse organisms and defined stage-specific and common cell types. For the planula and medusa stages in Clytia hemisphaerica we found both: cells, with unique transcriptional programs, and cell types with conserved gene expression programs between both stages. We could detect shared elements in the transcriptional signature between neural cells and mature nematocytes, allowing us to propose evolutionary scenarios about their emergence. Also, intending to reconstruct the evolution of the neural and secretory cell types at the aboral end of the cnidarian planula larva, we compared Clytia and the stony coral Pocillopora acuta. Also, we aimed to identify potential homologous cellular lineages in two species of Lophotrochozoan larvae.
The results of our research were published in high-impact peer-reviewed scientific journals and were presented at prestigious international conferences. Also, we organized several outreach activities to disseminate the results of our research to the general public.
The comparison of the data generated for the different species under study will help better understand the course of animal evolution.
In this project, we successfully developed a resource available to all partners and the interested public that allows easy access to standardized scRNA-seq datasets created within and outside the network. The resource allows on-site gene expression comparisons across cell types and diving into the evolutionary relationships of genes across a great number of species. This will be of great use for researchers interested in cell type evolution.
Our research on PIWIL1/piRNA pathway in cancer cells is of biomedical impact. Gaining a better understanding of the piRNA pathway during tumorigenesis can help identify molecules that might serve as new prognostic markers and therapeutic targets.
Lastly, we have designed an unprecedented type of science exhibition. Modern biological research often lacks physical objects to exhibit. The objects of interest are indirectly visible through a range of complicated technologies and long processes. To bridge the gap between the highly specialized EvoCELL science and the wider public we developed the virtual exhibition “Life: Through the Looking Glass”. The exhibition attempts to show the processual nature of science and the questions scientists pose as they research. It presents eight stories that let the viewer dive into the research journey of the EvoCELL scientists, and explore a realm with plenty of unknown elements.
In this project, we successfully developed a resource available to all partners and the interested public that allows easy access to standardized scRNA-seq datasets created within and outside the network. The resource allows on-site gene expression comparisons across cell types and diving into the evolutionary relationships of genes across a great number of species. This will be of great use for researchers interested in cell type evolution.
Our research on PIWIL1/piRNA pathway in cancer cells is of biomedical impact. Gaining a better understanding of the piRNA pathway during tumorigenesis can help identify molecules that might serve as new prognostic markers and therapeutic targets.
Lastly, we have designed an unprecedented type of science exhibition. Modern biological research often lacks physical objects to exhibit. The objects of interest are indirectly visible through a range of complicated technologies and long processes. To bridge the gap between the highly specialized EvoCELL science and the wider public we developed the virtual exhibition “Life: Through the Looking Glass”. The exhibition attempts to show the processual nature of science and the questions scientists pose as they research. It presents eight stories that let the viewer dive into the research journey of the EvoCELL scientists, and explore a realm with plenty of unknown elements.