Acoel single-cell transcriptomics: cell-type analysis of a deep branching bilaterian

Duruz, Jules; Kaltenrieder, Cyrielle; Ladurner, Peter; Bruggmann, Rémy; Martinez, Pedro; Sprecher, Simon G.

doi:10.1101/2020.07.10.196782

Cited by 4 publications

(3 citation statements)

References 65 publications

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“…However, the expression profiles of epidermal cells in Hofstenia did not reveal obvious shared differentiated markers with the epidermal cells of other bilaterians found within the Nephrozoa. Previous work in the acoel I. pulchra identified similar cell types to those we found in Hofstenia based on enrichment of genes associated with biological functions (Duruz et al, 2021). In addition to uncovering these molecular functions in the corresponding Hofstenia cell types, our dataset recovered transcription factors associated with these cell types.…”

Section: Discussionsupporting

confidence: 76%

Acoel single-cell atlas reveals expression dynamics and heterogeneity of a pluripotent stem cell population

Hulett

Kimura

Bolaños

et al. 2022

Preprint

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Pluripotent adult stem cell populations underlie whole-body regeneration in many distantly related animal lineages. These collectively pluripotent populations of cells share some features across species, such as the expression of piwi and other germline-related genes. Studies of how these cells operate during regeneration are needed in diverse systems to determine how underlying cellular and molecular mechanisms of renewal and differentiation compare. Here, we sought to characterize stem cells and their dynamics in the acoel Hofstenia miamia, a highly regenerative marine worm with a piwi-expressing stem cell population called neoblasts. Transcriptome profiling at single cell resolution revealed cell types shared across postembryonic stages, including stem cells and differentiated cell types such as neural, epidermal, muscle, and digestive cells. Reconstruction of single-cell differentiation trajectories followed by functional studies confirmed that neoblasts are the source of differentiated cells and identified transcription factors needed for the formation of major cell types. Next, analysis of single-cell transcriptomes from regenerating worms showed that both differentiated cells and stem cells dynamically alter gene expression in response to amputation. Further analysis of the stem cells recovered subpopulations of neoblasts, each with specific transcriptional profiles suggesting that the majority of neoblasts are specialized to differentiated lineages, reflecting putatively lineage-primed progenitors. Notably, neoblast subsets in Hofstenia were identifiable consistently across postembryonic stages and also displayed differential expression dynamics in response to wounding. Altogether, these data suggest that whole-body regeneration is accomplished by the coordination of cells with distinct and dynamic transcriptomic profiles through time. Furthermore, the data generated here will enable the study of how this coordination is achieved, enhancing our understanding of pluripotent stem cells and their evolution across metazoans.

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Section: Discussionsupporting

confidence: 76%

Acoel single-cell atlas reveals expression dynamics and heterogeneity of a pluripotent stem cell population

Hulett

Kimura

Bolaños

et al. 2022

Preprint

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“…The ways in which these types of variables could affect stemness signatures should be considered. In addition to planarians (Platyhelminthes), reliable ASC transcriptomes exist for species in diverse phyla including Porifera [37], Cnidarians [38], Acoela [39,40], and Arthropoda [27], as well as for mammalian ESCs (Fig. 1A) [41,42].…”

Section: Determining Asc Gene Expression and Enrichmentmentioning

confidence: 99%

One stem cell program to rule them all?

Wiggans

Pearson

2020

The FEBS Journal

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Many species of animals have stem cells that they maintain throughout their lives, which suggests that stem cells are an ancestral feature of all animals. From this, we take the viewpoint that cells with the biological properties of 'stemness'-self-renewal and multipotency-may share ancestral genetic circuitry. However, in practice is it very difficult to identify and compare stemness gene signatures across diverse animals and large evolutionary distances? First, it is critical to experimentally demonstrate self-renewal and potency. Second, genomic methods must be used to determine specific gene expression in stem cell types compared with non-stem cell types to determine stem cell gene enrichment. Third, gene homology must be mapped between diverse animals across large evolutionary distances. Finally, conserved genes that fulfill these criteria must be tested for role in stem cell function. It is our viewpoint that by comparing stem cell-specific gene signatures across evolution, ancestral programs of stemness can be uncovered, and ultimately, the dysregulation of stemness programs drives the state of cancer stem cells.

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“…We find Xenoturbella neurons to be significantly less diverse than those characterized in acoelomorphs 31 , another of the Xenacoelomorph lineages. Interestingly, Xenoturbella neurons express hallmarks of metazoan neurons including islet-1, brn3/pouIV and the proneural bHLH transcription factor achaete-scute, indicating that they share some features of an ancestral neural regulatory program.…”

Section: Conserved Differentiators Of Neural and Muscle Cell Typesmentioning

confidence: 54%

Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage

Robertson

Sebé-Pedrós

Saudemont

et al. 2022

Preprint

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Evidence for a sister relationship between Xenacoelomorpha and Ambulacraria (Xenambulacraria) has revived the longstanding debate surrounding the complexity of the Urdeuterostomian and Urbilaterian ancestors and has led to a reassessment of early bilaterian features. Employing whole organism singlecell RNA-seq in the marine xenacoelomorph worm Xenoturbella bocki, we show that Xenambulacrarian nerve nets share regulatory features and a peptidergic identity with those found in cnidarians and protostomes. We also suggest that Xenacoelomorpha muscles are likely to have evolved their smooth phenotype convergently. Furthermore, we identify pigmented cells as a potential synapomorphy of the Xenambulacraria. Taken together, these data are consistent with a simplification from an ancestral urbilaterian/urdeuterostomian body plan and a non-centralized nerve net, minimally differentiated contractile cells and evidence of deuterostome cell-type synapomorphies.

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Acoel single-cell transcriptomics: cell-type analysis of a deep branching bilaterian

Cited by 4 publications

References 65 publications

Acoel single-cell atlas reveals expression dynamics and heterogeneity of a pluripotent stem cell population

Acoel single-cell atlas reveals expression dynamics and heterogeneity of a pluripotent stem cell population

One stem cell program to rule them all?

Single cell atlas of Xenoturbella bocki highlights the limited cell-type complexity of a non-vertebrate deuterostome lineage

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