Less is more: Single Cell Analysis of Zebrafish Blood Development

Informazioni relative al progetto

ZF_Blood

ID dell’accordo di sovvenzione: 677501

DOI

10.3030/677501

Progetto chiuso

Data della firma CE 16 Febbraio 2016

Data di avvio 1 Maggio 2016

Data di completamento 30 Aprile 2022

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 500 000,00

Contributo UE

€ 1 500 000,00

Coordinato da

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

Periodic Reporting for period 4 - ZF_Blood (Less is more: Single Cell Analysis of Zebrafish Blood Development)

Periodo di rendicontazione: 2020-11-01 al 2022-04-30

Sintesi del contesto e degli obiettivi generali del progetto

Blood stem cells need to both perpetuate themselves (self-renew) and differentiate into all mature blood cells to maintain blood formation throughout life. However, it is unclear how the underlying gene regulatory network maintains this population of self-renewing and differentiating stem cells, and how it accommodates the transition from a stem cell to a mature blood cell. Our current knowledge of transcriptomes of various blood cell types has mainly been advanced by population-level analysis. However, the population of seemingly homogenous blood cells may include many distinct cell types with substantially different transcriptomes and abilities to make diverse fate decisions. To overcome these limitations, we used single-cell transcriptome sequencing of blood cells to reconstruct the regulatory networks that maintain the dynamic balance between different blood cell types. This was achieved by pursuing two main objectives:
1) To create a comprehensive atlas of single cell gene expression in blood cells and computationally reconstruct the blood lineage tree. We ordered cells according to their most likely developmental chronology and identified genes and gene regulatory networks that define distinct cell types.
2) The in-depth functional characterisation of a subset of novel key regulators of blood formation and identified cell types in vivo.
The results from these studies revealed complex relationships between the continuous spectra of blood cells, and provided unprecedented insight into the regulation of blood cell formation.

Lavoro eseguito dall’inizio del progetto fino alla fine del periodo coperto dalla relazione e principali risultati finora ottenuti

My group applies an integrative strategy, combining genetic perturbation with novel computational sequencing and network analysis methods to reconstruct and validate gene regulatory networks in blood development. The most important results include:

1. Resolving the cellular hierarchy of lineage development and progression in haematopoiesis in zebrafish (Cell Rep. 2016; Nat Commun. 2017). The results from these two studies have advanced our understanding of how haematopoietic cell fate decisions are instigated and provided significant new understanding of the architecture and functioning of lower vertebrate haematopoiesis. In addition, I have generated a user-friendly cloud repository, BASiCz (Blood Atlas of Single Cells in zebrafish) for interactive exploration and visualisation of single-cell sequencing data from zebrafishblood cells (http://www.sanger.ac.uk/science/tools/basicz).
2. Development of a novel zebrafish model for the study of the rare haematological disorder Fanconi anaemia. The generated model was used to understand the underlying disease biology (PNAS 2017).
3. Characterisation of T and NK cells at the single-cell transcriptome level for the first time in a non- mammalian species. We proposed a model of high gene turnover and faster evolution of immune transmembrane genes, but at the same time conservation of core cytoplasmic immune genes from zebrafish to mammalian species (Genome Res. 2017). In addition, we were the first group to identify and characterise innate-lymphoid cells (ILCs) in zebrafish (Sci Immunol. 2018).
4. Characterised transcriptional, epigenetic and mutational changes that occur during differentiation of blood stem cells (Cell Stem Cell 2021, Nature 2021).

Progressi oltre lo stato dell’arte e potenziale impatto previsto (incluso l’impatto socioeconomico e le implicazioni sociali più ampie del progetto fino ad ora)

Together with collaborators, my group has pioneered the use of somatic mutations to
i) estimate the rate and time of mutation acquisition during normal development,
ii) reconstruct blood phylogenetic tree during development and,
iii) estimate the number of blood antecedents at different stages during development. In addition, we characterised transcriptional and epigenetic changes that occur during differentiation of blood stem cells. All these achievements significantly advanced a research field and went beyond the state of the art.

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