title: Molecular cell fate decisions in the sea anemone Nematostella vectensis resolved by a developmental single-cell RNA-seq atlas
Creators: name: Steger, Julia
Publisher: name: :none
Year: 2024

description: Zelltyp-spezifische Regulationsprogramme steuern Entscheidungen über das Zellschicksal, von der anfänglichen Spezifikation bishin zur Identität des terminal differenzierten Zelltyps. In diesem Zusammenhang weist die Seeanemone Nematostella vectensis mehrere Merkmale auf, die Einblicke in die Entwicklung und Evolution von Zelltypdiversität ermöglichen. Die phylum-definierenden Nesselzellen (Cnidozyten) bieten die einzigartige Gelegenheit, die molekularen Mechanismen zu untersuchen, die evolutionärer Neuheit zugrunde liegen. Aufgrund der langen Lebensdauer müssen alle Zelltypen ständig ersetzt werden. Aus diesem Grund besteht das Kernstück meines PhD-Projektes in der Erstellung und Analyse eines Einzelzelltranskriptom-Atlasses der Entwicklung von Nematostella. Durch die Sequenzierung eines dichten Zeitverlaufs von Einzelzelltranskriptomen durch den gesamten Lebenszyklus, von Embryogenese zu Homöostase, habe ich einen umfassenden single-cell RNA-seq Atlas erstellt. Auf der Grundlage der enthaltenen Entwicklungsverläufe konnten die Beziehungen zwischen allen Zelltypen,  differenzierten und undifferenzierten, charakterisiert werden. Ein Schwerpunkt meiner Dissertation liegt auf der neuroglandulären Linie, da meine Daten enge Beziehungen zwischen Neuronen und Drüsenzellen aufdecken, und SoxC als upstream Regulator identifiziert werden konnte. Weiters analysierten wir auch die molekularen Mechanismen, die zur Diversifizierung des Muskelzellkomplements geführt haben, und beschreiben Ähnlichkeiten zwischen den regulatorischen Programmen von Tentakelretraktormuskelzellen und Neuronen. Wir konnten nachverfolgen, dass diese Population von Muskelzellen und neuroglanduläre Zellen von einer multipotenten Progenitorpopulation abstammen, was zeigt, dass das Entwicklungspotenzial der "neuralen" Progenitoren größer ist als bisher angenommen. Diese Erkenntnis führte zu einer Untersuchung von Transkriptomsignaturen, die auf das Vorhandensein von Stammzellen in hinweisen. Wir konnten die Expression des Keimbahn-assoziierten Gens Nanos2 in Keimbahn- und somatischen Zelltypen nachweisen, was die Existenz von multipotenten Stammzellpopulationen in Nematostella bekräftigt.
description: Cell type-specific regulatory programs direct processes from fate specification to the maintenance of terminal cell type identities. Along the underlying developmental pathways, cells transition through a diversity of intermediate transcriptome states. Whether trajectories active during early development also regulate the replacement of cell types during homeostasis, or if distinct mechanisms are switched on, is currently unknown. To explore the gene regulatory programs of early metazoan cell types, the phylum Cnidaria holds an informative position. The cnidarian and bilaterian lineages are sister groups and have been evolving independently for about 600 million years. Therefore, comparative analyses of cell type-specific molecular signatures between these two groups are informative about the early evolution of transcriptional gene regulation. In addition, Cnidarians have long life spans, and cells have to be replaced continuously. The cnidarian cell type complement includes functionally specialised myocytes, neurons, and gland cells. In addition, stinging cells (cnidocytes) are the phylum-defining feature and offer the unique opportunity to investigate the molecular mechanisms driving the generation of a novel cell type. For a comprehensive understanding of central aspects of cell type development and evolution, we performed whole-organism single-cell transcriptomics throughout the life cycle of the starlet sea anemone Nematostella vectensis. The generation and analysis of this developmental single-cell RNA-seq atlas is the core of my PhD project. It resolves the differentiation trajectories of diverse cell types and allows to study their developmental and evolutionary relationships. In the scope of this thesis, I summarise and discuss some of our key findings that expand the current understanding of the population structure in Nematostella. Starting at the putative origin of cell type specification, we describe a multipotent Nanos2/Piwi1 population that gives rise to germline and somatic lineages, indicating a position at the very top of the differentiation cascade. The next focus is on the neural progenitor population. We identify SoxC as a master regulator of its specification, acting upstream of SoxB2. Originally, the known complement of NPC-derivatives included cnidocytes and neurons, but we identify gland cells and likely also tentacle retractor muscle cells as additional daughter cell types. This demonstrates that the developmental potential of the “neural” progenitor population is higher than previously described and similar to the one of hydrozoan i-cells. Neurons and gland cells share a common regulatory signature, which suggests they have a shared developmental history. An in-depth characterisation of the myocyte complement reveals the mechanisms underlying its diversification. We resolve four transcriptomically distinct muscle cell types that contract at slow or fast speed, depending on the differential usage of paralogous effector genes. In the two fast-contracting retractor muscle cell types, the similar effector gene sets are regulated by divergent regulatory signatures. Here, we identify anthozoan-specific expansions of bHLH transcription factors as drivers of fast muscle cell individuation. This developmental scRNA-seq atlas generated in the scope of my PhD allowed us to explore a diversity of novel findings. Hopefully, it will also provide a robust resource to the Nematostella community to advance our understanding of metazoan cell type evolution.