Cell lineages across scales, space and time

07 - 08 May 2024 09:00 - 17:00 Edgbaston Park Hotel
Segmented cells of a zebrafish embryonic retina

Theo Murphy meeting organised by Dr Giulia LM Boezio, Dr Afnan Azizi, Dr Claudio Cortés and Dr John Russell.

Lineage trajectories and cellular decisions coordinate embryonic development and growth. Similarly, cellular origin and clonal trajectories are crucial elements to understanding and modulating the response to injury, disease, and therapies. This meeting will showcase cutting-edge research spanning developmental biology, organ regeneration, and cancer, in light of recently developed techniques to study lineage trajectories and cellular decisions. 

The schedule of talks and speaker biographies will be available soon. Speaker abstracts will be available closer to the meeting date.

Poster session and short talks

There will be a poster session on Tuesday 7 May. If you would like to apply to present a poster, please submit your proposed title, abstract (not exceeding 200 words and in the third person), author list, name of the proposed presenter, and institution to the Scientific Programmes team no later than Monday 15 April.

We also welcome applications for short talks with the same abstract. Please indicate with your abstract submission if you wish to present your findings in a short talk.

Include the text 'Abstract submission - Cell lineage' in the email subject line. Please note that spaces are limited, and the selection of posters and presentations will be at the discretion of the scientific organisers.

Attending this event

This event is intended for researchers in relevant fields, and is a residential meeting taking place at the Edgbaston Park Hotel and Conference Centre, 53 Edgbaston Park Road, Birmingham, B15 2RS.

  • Free to attend
  • Advance registration essential (please request an invitation)
  • This is an in person meeting
  • Catering options are available to purchase during registration. Participants are responsible for their own accommodation booking.

Enquiries: contact the Scientific Programmes team

Organisers

  • Giulia Borezo

    Dr Giulia LM Boezio, The Francis Crick Institute, UK

    Giulia Boezio is a postdoctoral researcher in the Developmental Dynamics lab at the Francis Crick Institute, London. She obtained a MSc in Molecular Biology from the University of Milan (Italy) with a thesis focusing on Sox transcription factor control of zebrafish angiogenesis. For her PhD, she joined the lab of Didier Stainier at the Max Planck Institute for Heart and Lung Research, in Germany, to study intercellular and intertissue crosstalk in the context of heart development in zebrafish. For her postdoctoral research, Giulia joined James Briscoe’s lab to continue pursuing her interest in developmental biology and organ formation. In particular, she now focuses on understanding the lineage trajectories and the principles of cell fate commitment in the spinal cord, using a combination of imaging and genomics lineage tracing tools in chicken embryos and human embryonic tissues.

  • Afnan Azizi

    Dr Afnan Azizi, King’s College London and The Francis Crick Institute, UK

    Afnan obtained a BSc in Biochemistry with a minor in Mathematics and an MSc in Cellular and Molecular Medicine from University of Ottawa, Canada. He then moved to the University of Cambridge to pursue his PhD in the laboratory of Professor Bill Harris, looking at the role of interkinetic nuclear migration in morphogenesis of the vertebrate retina. He is now a postdoctoral fellow at King’s College London and The Francis Crick Institute working between the Houart and Guillemot laboratories to tackle the problem of how the human brain is formed at early embryonic stages and how it is different from that of other vertebrates, using 3D microscopy of intact tissue, single cell transcriptomics, and brain organoids. 

  • Dr John Russell, Cambridge University, UK

  • Claudio Cortes

    Dr Claudio Cortés, University of Oxford, UK

    Dr Cortes is fascinated by how cells move and how tissues/organs acquire their shape. He is particularly interested in mechanobiology  and how biological systems encode their exquisite complexity, using the embryonic heart as a model. He focuses on live imaging and modeling cell behaviour, using human, mouse and in-vitro models. He’s currently based in the University of Oxford. 

Schedule

Chair

Afnan Azizi

Dr Afnan Azizi, King’s College London and The Francis Crick Institute, UK

09:00-09:05 Introduction
Dr Giulia LM Boezio, The Francis Crick Institute, UK

Dr Giulia LM Boezio, The Francis Crick Institute, UK

09:10-09:40 Principles of Neural Stem Cell Lineage Progression

The concerted production of the correct number and diversity of neurons and glia by neural stem cells is essential for intricate neural circuit assembly. In the developing cerebral cortex, radial glia progenitors (RGPs) are responsible for producing all neocortical neurons and certain glia lineages. Clonal analysis by exploiting the single cell resolution of the genetic MADM (Mosaic Analysis with Double Markers) technology revealed an inaugural quantitative framework of RGP behaviour in the developing neocortex. However, the cellular and molecular mechanisms controlling RGP lineage progression through proliferation, neurogenesis and gliogenesis remain largely unknown. To this end we use quantitative MADM-based experimental paradigms at single RGP resolution to define the cell-autonomous functions of candidate genes and signalling pathways controlling RGP-mediated neuron and glia genesis. Ultimately, our results shall translate into a deeper understanding of brain function and why human brain development is so sensitive to the disruption of particular signalling pathways in pathological neurodevelopmental and psychiatric disorders.

Professor Simon Hippenmeyer, Institute of Science and Technology, Austria

Professor Simon Hippenmeyer, Institute of Science and Technology, Austria

09:40-10:10 Cell lineages in development and evolution

During embryogenesis, numerous cell lineages arise from a common progenitor and, along the ontogeny, diversify, interact with each other, integrate, and jointly build high-dimensional phenotypes. Our group employs the development of the face as a model to study cell lineages, their dynamics and underlying molecular drivers. We focus on the neural crest cells (NCCs) that give rise to an array of cell types and are essential contributors to facial morphogenesis. How the neural crest cells maintain the multipotency and commit to different fates was recently reassessed using new technologies. 

We employed single-cell transcriptomics to explore how multipotent NCCs make decisions and how the progression of NCC-derived lineages is coordinated along facial development. With this knowledge, we aim to reconstruct and compare the developmental history of the face in different species and identify evolutionary mechanisms altering development (such as heterochrony and heterotopy) to understand how morphological variation arises. 

I will also briefly mention how detailed knowledge of cell lineages enables better insight into the evolution of cell types. Here, we employ single-cell transcriptomes of skeletogenic lineage (cells forming cartilage and bone) with genomic phylostratigraphy (gene birth-dating) to reveal the assembly of cell type-specific gene expression programs. We provide evidence for the evolution of ancestral skeletogenic cell type at the onset of Bilateria and demonstrate the subsequent transcriptome elaboration and individuation. In particular, we show that taxon-restricted genes enabled the cells to control ancient functions and gave rise to the osteoblasts and hypertrophic chondrocytes. Interestingly, our analyses suggest that chondrocyte hypertrophy (thus endochondral ossification) evolved earlier than previously believed, which is supported by the recently discovered fossil evidence.

Dr Markéta Kaucká, Max Planck Institute for Evolutionary Biology, Germany

Dr Markéta Kaucká, Max Planck Institute for Evolutionary Biology, Germany

10:10-10:40 Regulation of temporal patterning in the developing retina

The generation of cell diversity and neural circuit assembly in the central nervous system requires precise spatiotemporal coordination of mechanisms regulating cell proliferation, specification, and differentiation. While much progress has been made in the last decades to elucidate how neural progenitors choose between alternative fates at any given time during development, much less is known about the mechanisms regulating how progenitors change over time to generate the right cell types at the right time. To study this question, Professor Cayouette and team use the mouse retina as a model system, where multipotent retinal progenitors give rise to seven major classes of retinal cell types in a precise chronological order. In this seminar, Professor Cayouette will present their latest work identifying a conserved cascade of transcription factors that encode temporal identity in mouse retinal progenitors. Their data indicate that these factors are necessary and sufficient to generate retinal cell types associated with their temporal window of expression. Professor Cayouette will also present recent results showing that temporal identity factors can reprogram terminally differentiated glia into neuron-like cells, bridging the concept of temporal patterning with somatic cell state maintenance. 

Professor Michel Cayouette, Montreal Clinical Research Institute (IRCM) and Université de Montréal, Canada

Professor Michel Cayouette, Montreal Clinical Research Institute (IRCM) and Université de Montréal, Canada

10:40-11:00 Break
11:00-11:30 Horizontal gene transfer in transmissible cancer

Although somatic cell genomes are usually entirely clonally inherited, sporadic exchange of nuclear DNA between cells of an organism by a process of cell fusion, phagocytosis, or through other mechanisms, can occur. This phenomenon has long been noted in the context of cancer, where it could be envisaged that horizontal gene transfer plays a functional role in disease evolution. However, an understanding of the frequency and significance of this process in naturally occurring tumours is lacking. I will describe the results of a screen that searched for horizontal gene transfer in transmissible cancers occurring in dogs and Tasmanian devils.

Professor Elizabeth Murchison, University of Cambridge, UK

Professor Elizabeth Murchison, University of Cambridge, UK

11:30-12:30 3x selected from abstracts
12:30-13:30 Lunch

Chair

Giulia Borezo

Dr Giulia LM Boezio, The Francis Crick Institute, UK

13:30-14:00 Single-cell multi-omics map of human foetal blood in Down's Syndrome

Down’s Syndrome (DS) predisposes individuals to haematological abnormalities, such as increased number of erythrocytes and leukaemia in a process that is initiated before birth and is not entirely understood. To understand dysregulated haematopoiesis in DS, we integrated single-cell transcriptomics of over 1.1 million cells with chromatin accessibility and spatial transcriptomics datasets using human foetal liver and bone marrow samples from three disomic and 15 trisomic foetuses. We found that differences in gene expression in DS were both cell type- and environment-dependent. Furthermore, we found multiple lines of evidence that DS haematopoietic stem cells (HSCs) are “primed” to differentiate. We subsequently established a DS-specific map linking non-coding elements to genes in disomic and trisomic HSCs using 10X Multiome data. By integrating this map with genetic variants associated with blood cell counts, we discovered that trisomy restructured regulatory interactions to dysregulate enhancer activity and gene expression critical to erythroid lineage differentiation. Further, as DS mutations display a signature of oxidative stress, we validated both increased mitochondrial mass and oxidative stress in DS and observed that these mutations preferentially fell into regulatory regions of expressed genes in HSCs. Altogether, our single-cell, multi-omic resource provides a high-resolution molecular map of foetal haematopoiesis in Down’s Syndrome and indicates significant regulatory restructuring giving rise to co-occurring haematological conditions.

14:00-14:30 High-resolution mapping of cell lineages during mammalian embryogenesis

Understanding the routes through which a single cell populates the adult organism is one of the most fundamental yet elusive areas of biology. In recent years, immense progress has been made in cataloguing cell identity during mouse development through single-cell RNA sequencing, though these data alone do not shed light on the ancestry and fate choices taken by cells. To address this, we have recently developed and published new mouse models, named CARLIN and DARLIN, that use CRISPR-mediated cellular barcoding to trace thousands of cells in vivo with unique, transcribed tags in an inducible manner. Using these systems, we have mapped the clonal and anatomical origins of the hematopoietic system. Our data demonstrate the existence of diverse embryonic origins for both foetal and long-lived blood cells and shed light on the drivers of hematopoietic heterogeneity in adult tissues. Furthermore, we have generated single-cell RNA sequencing libraries of whole barcoded early mouse embryos, allowing us to create a blueprint of lineage decisions taken by cells during gastrulation. Our work sheds light on long-standing questions in developmental biology and can be used to understand the cell-of-origin of paediatric diseases, and to bring insight into very basic biological questions concerning cell fate commitment.

Dr Sarah Bowling, Stanford University School of Medicine, USA

Dr Sarah Bowling, Stanford University School of Medicine, USA

14:30-15:00 Next-generation lineage and circuit tracing to uncover principles of neuronal network assembly

Mammalian brain development involves the generation of many neuronal and non-neuronal cell types from a presumably small pool of progenitor cells. Single-cell RNA-seq has been widely used for building cell type atlases of developing and adult brains, but the lineage relationships between mature cell types and progenitor cells are not well understood. I will present our efforts for massively parallel in vivo barcoding of early progenitors to profile gene expression and clonal relations with single-cell and spatial transcriptomics. I will demonstrate how this technology can be used to reveal clonal divergence and convergence across different cell classes in the mouse forebrain and discuss our recent findings on clonally inherited gene expression patterns in the mouse cortex. Finally, I will discuss how cellular barcoding approaches could be utilized for high density tracing of synaptic networks.

Dr Michael Ratz, Karolinska Institutet, Sweden

Dr Michael Ratz, Karolinska Institutet, Sweden

15:00-15:30 Break
15:30-15:45 1x selected from abstracts
15:45-16:15 Recording Notch signaling activity during brain development

CRISPR/Cas genome editing tools and scRNA-seq have been combined for clonal tracing and lineage tree reconstruction with cell type resolution. We reasoned that CRISPR-Cas molecular recorders can be adapted to investigate a new biological paradigm – signal transduction during development. Briefly, the system works as follows: when a cell receives sufficient input from a signalling source of interest, Cas protein expression is activated and induces irreversible mutations to a genomic CRISPR barcode array. The edits permanently mark cells and their progenies, maintaining a record of the signalling events over time. The edited barcodes are expressed as mRNA and sequenced at single-cell resolution together with the cell’s transcriptome. Thus, the transcriptional identity of the cell, its lineage and a record of signalling history are simultaneously determined. This technology, SABER-seq (signal-activated barcode editing recorder), is a novel platform for rapid, scalable and high-resolution mapping of brain-wide signalling activity during development. We applied SABER-seq to record Notch signalling in developing zebrafish brains. SABER-seq has two components: a signalling sensor and a barcode recorder. The sensor activates Cas9 in a Notch-dependent manner with inducible control while the recorder accumulates mutations that represent Notch activity in founder cells. The Notch pathway regulates neural cell fates. However, our understanding of its roles in various neural sublineages and developmental windows is not complete. We are investigating which neuron subtypes and progenitor classes are derived from ancestors stimulated by the Notch pathway. We anticipate our method will be broadly applicable to other signalling pathways and disease states.

Dr Bushra Raj, University of Pennsylvania, USA

Dr Bushra Raj, University of Pennsylvania, USA

16:20-18:40 1min posters flash talks
16:40-20:15 Poster session

Chair

Dr John Russell, Cambridge University, UK

09:00-09:05 Welcome to day 2
09:05-09:40 Digital ascidian embryos: natural variation and the logical rules of animal embryogenesis

Ascidians are marine invertebrates which belong to the vertebrate sister group. While adult ascidians show remarkable regenerative capacities, their embryos seem to be living on a different planet: they develop without growth or apoptosis, with a quasi-invariant cell lineage, conserved since the emergence of the group around 400 MY ago (Lemaire, 2011). Ascidian genomes, however, evolve particularly rapidly. 

To understand how distinct ascidian species can form very similar embryos despite the divergence of their genomes, we are combining experimental, mathematical, and physical approaches (e.g., Guignard, Fiuza et al., 2020). During the talk, I will present our ongoing efforts to quantify natural variation within and between species during ascidian embryonic development, and our expectation of what natural variation in ascidian embryonic development could tell us more generally about the logic of animal embryonic development. Our analyses include methods to measure distances between cell lineages within and across embryos.

Dr Patrick Lemaire, Centre de Recherche en Biologie cellulaire de Montpellier, France

Dr Patrick Lemaire, Centre de Recherche en Biologie cellulaire de Montpellier, France

09:40-10:10 Tracking the origin of cancer in space and time

Oncogenic mutations are abundant in tissues of healthy individuals, but rarely form tumours. Yet, how healthy tissue organization and dynamics may impact on the fate of these mutant cells remains unclear. Using the mammary gland as a model, we try to resolve these mechanisms. Making use of lineage tracing and (intravital) imaging approaches, we trace the fate of epithelial cells that acquire oncogenic mutations in their intact environment. We find that tissue hierarchy and dynamics, such as oestrous cycle driven remodelling, pregnancy and lactation, impact on mutant cell fate and behaviour. Interestingly, the impact of tissue remodelling is oncogene dependent, and may either be protective against or promoting mutant cell survival and spread. For example, in the context of Brca1-/-Trp53-/- cells, we find that rounds of local tissue remodelling, driven by the oestrous cycle leads to the stochastic and collective loss of mutant cells throughout the epithelium, and the elimination of the majority of mutant clones. However, it simultaneously enables a minority of mutant clones, that by chance survive, to geometrically expand. This expansion leads to cohesive fields of mutant cells spanning large parts of the mammary ducts. Eventually, this process of clone expansion becomes restrained by the one-dimensional geometry of the ducts, limiting uncontrolled colonization. Together, we reveal layers of protection that serve to eliminate mutant cells in healthy tissues, at the expense of the expansion of a minority of cells, which may spread, thereby predisposing the tissue to transformation. 

Dr Colinda Scheele, VIB-KU Leuven Centre for Cancer Biology, Belgium

Dr Colinda Scheele, VIB-KU Leuven Centre for Cancer Biology, Belgium

10:10-10:40 PhOTO-Bow: An optical lineage-tracing system combining single-cell tracking with clonal analysis

Tracking the fate of individual cells and their progeny through lineage tracing has been widely used to investigate various biological processes including embryonic development, homeostasis, regeneration, and disease. Fluorescent reporter-based lineage tracing approaches based on the original 'Brainbow' method, which mark each cell with various colour combinations, have been fundamental to our understanding of developmental biology and stem cell research. Although they have provided impressive insights into cell dynamics, they have disadvantages: the Cre–loxP recombination event does not lead to instantaneous cell labelling, which makes precise spatiotemporal tracking of a cell population from the clonal founder challenging. Here, the scientists designed an optical lineage-tracing system, termed PhOTO-Bow, which combines the beneficial features of primed conversion(1-8) of photoconvertible fluorescent proteins (precise and instantaneous cell labelling for single-cell tracking) with the Brainbow system (indelible labelling for identification of all progenies of a single cell). The PhOTO-Bow system fulfils the requirements to establish comprehensive lineage trees and can infer much needed spatiotemporal axes for reconstructing cell state transitions during development and disease.

Dr Periklis (Laki) Pantazis, Imperial College London, UK

Dr Periklis (Laki) Pantazis, Imperial College London, UK

10:40-11:00 Break
11:00-11:30 Deconstructing an organ architecture - multicolour cell labelling in the liver

Organs depend on highly specialized architectures to perform their distinctive functions. Yet, for most tissues it is poorly understood how progenitors self-organize in vivo to establish the functional 3D tissue organization during development. We investigate this fundamental question focusing on the vertebrate liver, which in addition has the capacity to rebuild its architecture following injury. In the liver, hepatocytes are the main cell type and are arranged between the vascular and biliary ductal networks. In addition, hepatocytes connect apically with small canaliculi to the terminal branches of the biliary network. Despite the importance for hepatic function, little is known about cell type ratios and how they subsequently arrange in 3D. We employ the transparency of zebrafish embryos combined with novel lineage tracing tools and live-imaging to capture the cell behaviours and tissue interactions directing the progenitor-to-functional 3D-architecture transition at single cell resolution. Findings of how the correct cell type proportions for a functional tissue organization are set up, and how hepatocytes connect to the biliary system, including novel modes of cell-cell communication between different hepatic cell types will be presented. Such insights will aid our understanding of congenital bile duct abnormalities and further generating 3D functional hepatic architecture by tissue engineering approaches.

Dr Elke Ober, FAU Erlangen-Nürnberg, Germany

Dr Elke Ober, FAU Erlangen-Nürnberg, Germany

11:30-12:15 3x selected from abstracts
12:20-13:30 Lunch

Chair

Claudio Cortes

Dr Claudio Cortés, University of Oxford, UK

13:30-14:00 Regeneration at your fingertips: the role of the extracellular matrix

While some vertebrates are able to regenerate their appendages, this regenerative capacity is limited in mammals. Remarkably, the distal portion of the mammalian digit tip can regenerate following amputation. In contrast, amputations further along the finger or toe, removing critical structures such as the nail unit, results in fibrosis. The cues that direct one wound recovery process instead of the other is largely unknown. Our work examines the role of the extracellular matrix (ECM) element hyaluronic acid (HA) in promoting regeneration in mice. Through single-cell transcriptomics and immunohistochemistry, we discovered that regenerating stromal cells construct an ECM niche that harbours markedly more cross-linked, aggrecan-HA complexes. This is critical for forming pericellular coats of ECM called the glycocalyx, which can drastically alter the mechanical microenvironment and ligand binding to cell-surface receptors. Knockdown of hyaluronic acid using 4-methylumbelliferone leads to a wound healing response that resembles a non-regenerative amputation. Through in situ and in vitro studies we explore the mechanisms which inhibit regeneration from a tissue mechanics level and propose that a hyaluronic acid-rich environment can promote responsiveness to regenerative cues such as BMP signalling. Altogether, our work identifies a major difference in HA response in the regenerative ECM niche, which if therapeutically augmented, may be able to improve wound healing and mitigate fibrosis.

Dr Mekayla Storer, Cambridge University, UK

Dr Mekayla Storer, Cambridge University, UK

14:00-14:30 Barcoding the mouse germline clones from development to the next generation

Germline is the only cell lineage transmitted to the next generation. De novo mutations occurring in germline will be conveyed by sperm and eggs to the next generation. However, albeit being critical for transmitting the mutations, germline cells’ clonal dynamics remains underexplored in mammals. Using a DNA barcoding methodology, Professor Yoshida and team are analysing the clonal lineage behaviour of the entire germ cell population in male mice – from their initial population in early embryos through migrating primordial germ cells, sex determination, spermatogonial stem cell establishment and maintenance, leading to spermatogenesis. They further analysed the transmission of barcoded genomes to the next generation. Professor Yoshida and team found that a considerable fraction of clones are extinct during early development, while those surviving this stage maintain their clonal diversity until adulthood, proportionally transmitted to the next generations. Professor Yoshida will discuss the potential significance and cellular mechanisms underlying these observed clonal dynamics.

Professor Shosei Yoshida, National Institute for Basic Biology, Japan

Professor Shosei Yoshida, National Institute for Basic Biology, Japan

14:30-15:00 Fluctuating methylation as a high temporal-resolution molecular clock to track lineages in vivo.

In vitro cell barcoding methods are a powerful tool to track cell lineage relationships, but they are inappropriate for use in human clinical samples. To understand cancer evolution in vivo, we must instead rely on naturally occurring heritable lineage tracing markers that encode the evolutionary history of a population of cells. Here, Dr Gabbutt shall discuss his team’s recent work on identifying selectively neutral methylation sites and employing them as a molecular clock to characterise the evolutionary history of almost 2000 lymphoid cancers (Gabbutt et al, 2023).

Dr Calum Gabbutt, The Institute of Cancer Research, UK

Dr Calum Gabbutt, The Institute of Cancer Research, UK

15:00-15:30 Break
15:30-15:45 1x selected from abstracts
15:45-16:15 Dynamics of spermatogenic stem cell regulation

To replenish cells lost through exhaustion or damage, tissue stem cells must achieve a perfect balance between renewal and differentiation. To study the factors that control such fate asymmetry, emphasis has been placed on mechanisms in which stem cell competence relies on signals from a discrete anatomical niche. However, in many tissues, stem cell maintenance takes place in an open or facultative niche, where stem cells disperse among their differentiating progenies. Using mouse spermatogenesis as a model, we present evidence that stem cell density regulation relies on a feedback mechanism, reminiscent of “quorum sensing” in bacterial populations, in which cells transition reversibly between states biased for renewal and primed for differentiation. Using a modelling-based approach, we show that this mechanism provides predictive insights into stem cell dynamics during steady-state, as well as under perturbed and transplantation conditions. We discuss the potential implications of these findings for the regulation of stem cell density in other epithelial contexts, as well as their ramifications for the elucidation of dynamic information from single-cell gene expression profiling data.

Professor Ben Simons, University of Cambridge, UK

Professor Ben Simons, University of Cambridge, UK

16:15-17:00 Panel discussion and future perspectives