Biology subjects

Emili, E.

Publications and source records attributed to Emili, E..

4 recordsLinked to original sources

bioRxiv2024

The Hydractinia cell atlas reveals cellular and molecular principles of cnidarian coloniality

Coloniality is a widespread growth form in cnidarians, tunicates, and bryozoans, among others. Despite being modular, composed of multiple zooids and supporting tissues, colonies function as a single physiological unit. A major question in the biology of colonies is the cellular mechanism of generating structurally and functionally distinct colony parts. The cnidarian Hydractinia establishes colonies with different types of zooids (polyps), interconnected by a gastrovascular system that is attached to the substrate and known as stolons. We obtained single cell transcriptomic profiles of [~]200K Hydractinia cells, including isolated stolons and two polyp types. We characterised the major Hydractinia cell types and quantified their abundance across colony parts. Overall, we find that distinct colony parts are characterised primarily by distinct combinations of shared cell types and to a lesser extent by part-specific cell types. Therefore, we propose that both cell type combinations, as well as rarer cell type innovations, have been the main mechanism in the evolution of coloniality in cnidarians. We identified cell type-specific transcription factors (TFs) and gene networks expressed within these cell types. Notably, we discovered a previously unidentified, stolon-specific cell type, which expresses enzymes related to biomineralization and chitin synthesis, reminiscent of molluscan shell matrix proteins that may represent a crucial adaptation to the animals habitat. In summary, the Hydractinia cell atlas elucidates the fundamental cellular and molecular mechanisms underlying coloniality.

systems biology↗

bioRxiv2024

Multiplex single-cell analysis of serotonergic neuron function in planarians reveals widespread effects in diverse cell types

Neurons function by interacting with each other and with other cell types, often exerting organism-wide regulation. Serotonergic neurons play a systemic role in processes such as appetite, sleep and motor control. Functional studies in the planarian Schmidtea mediterranea have shown that impairment of serotonergic neurons results in systemic effects. Studying neurons and the tissues they interact with is challenging using either bulk or single-cell analysis techniques. While bulk methods merge the information from all cell types, single-cell methods show promise in overcoming this limitation. However, current single-cell approaches encounter other challenges including stress of cell dissociation, high cost, multiplexing capacity, batch effects, replication and statistical analysis. Here we used ACME and SPLiT-seq to generate a multiplex single-cell analysis of serotonergic neuron function in planarians by inhibiting pitx and lhx1/5-1, two transcription factors expressed in them. We recovered single-cell transcriptomic profiles of 47,292 cells from knockdown and control animals, including biological and technical replicates. Our results show that epidermal, muscular and the recently described parenchymal cell types are affected the most by serotonergic neuron impairment. By computationally dissecting each cell type, we elucidated gene expression changes in each, including changes in epidermis cilia genes and myofiber genes in muscle. Interestingly, parenchymal cells downregulate genes involved in neurotransmitter recycling, suggesting a glial-like function of these recently described enigmatic cell types. Our results will allow disentangling the complexity of serotonergic neuron inhibition by studying the downstream effectors and the affected tissues, and offer new data on the function of parenchymal cells in planarians. Ultimately, our results pave the way for dissecting complex phenotypes through multiplex single-cell transcriptomics.

systems biology↗

bioRxiv2023

Allometry of cell types in planarians by single cell transcriptomics

Allometry explores the relationship between an organisms body size and its various components, offering insights into ecology, physiology, metabolism, and disease. The cell is the basic unit of biological systems, and yet, the study of cell type allometry remains relatively unexplored. Single-cell RNA sequencing (scRNA-seq) provides a promising tool for investigating cell type allometry. Planarians, capable of growing and degrowing following allometric scaling rules, serve as an excellent model for such studies. We used scRNA-seq to examine cell type allometry in asexual planarians of different sizes, revealing that they consist of the same basic cell types but in varying proportions. Notably, the gut basal cells are the most responsive to changes in size, suggesting a role in energy storage. We capture the gene regulatory programs of distinct cell types in response to size. This research sheds light on the molecular and cellular aspects of cell type allometry in planarians and underscores the utility of scRNA-seq in such investigations.

systems biology↗

bioRxiv2023

Annelid adult cell type diversity and their pluripotent cellular origins

Annelids are a broadly distributed, highly diverse, economically and environmentally important group of animals. Most species can regenerate missing body parts, and many are able to reproduce asexually. Therefore, many annelids can generate all adult cell types in adult stages. However, the putative adult stem cell populations involved in these processes, as well as the diversity of adult cell types generated by them, are still unknown. Here, we recover 75,218 single cell transcriptomes of Pristina leidyi, a highly regenerative and asexually-reproducing freshwater annelid. We characterise all major annelid adult cell types, and validate many of our observations by HCR in situ hybridisation. Our results uncover complex patterns of regionally expressed genes in the annelid gut, as well as neuronal, muscle and epidermal specific genes. We also characterise annelid-specific cell types such as the chaetal sacs and globin+ cells, and novel cell types of enigmatic affinity, including a vigilin+ cell type, a lumbrokinase+ cell type, and a diverse set of metabolic cells. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. In these piwi+ cells, we also find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors. Finally, lineage reconstruction analyses reveal the existence of differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids for the first time and serve as a resource for studying annelid cell types and their evolution. On the other hand, our characterisation of a piwi+ cell population with a pluripotent stem cell signature will serve as a platform for the study of annelid stem cells and their role in regeneration.

genomics↗