Cell lineages across scales, space and time

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

Simon Hippenmeyer studied Molecular Biology and obtained a PhD in Neurobiology at Biozentrum, University of Basel, Switzerland. He was a postdoctoral fellow at Stanford University, USA. In 2012 he joined IST Austria (ISTA) as Assistant Professor and became Professor in 2019. Since 2020 he is also the Life Sciences Research Area Chair. His research focuses on fundamental neurobiological questions related to neural stem cell biology, neural development and circuit assembly. 

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

With a PhD in Animal Physiology and a master's degree in Molecular Biology and Genetics, Markéta moved to Sweden to conduct developmental biology research at Karolinska Institute. She revealed fundamental processes behind early head development and skull growth. Markéta did a second postdoc at the Centre for Brain Research at the Medical University Vienna to investigate the tight developmental link between the brain and skull formation. In 2019, Markéta was appointed an independent Group Leader at the Max Planck Institute for Evolutionary Biology in Germany. She leads the group Evolutionary Developmental Dynamics, and her research is at the intersection of Evo-Devo and molecular and cellular biology. Markéta employs an interdisciplinary skillset including single-cell omics, high-resolution and 3D imaging, bioinformatics and in vivo models to investigate the complex process of face formation and shaping, with a particular focus on how evolution altered these processes along vertebrate phylogeny. 

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

Michel Cayouette (PhD) is Director of the Cellular Neurobiology Research Unit and Vice-President, Research and Academic Affairs at the Montreal Clinical Research Institute (IRCM). He is also a Full Research Professor in the Department of Medicine at Université de Montréal, and Adjunct Professor in the Department of Anatomy and Cell Biology at McGill University. He is Director of the FRQS Vision Health Research Network, an initiative dedicated to promoting research capacity and international visibility for more than 140 vision scientists in Quebec. He is also Chief Scientific Advisor for Fighting Blindness Canada and member of the International Scientific Advisory Board of Institut de la Vision (Paris, France). His research focuses on the cellular and molecular mechanisms regulating nervous system development and regeneration, with a particular emphasis on the retina. 

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

Elizabeth Murchison is Professor of Comparative Oncology and Genetics at the University of Cambridge, Department of Veterinary Medicine. Her laboratory, the Transmissible Cancer Group, studies the genetics, evolution and host interactions of clonally transmissible cancers in dogs and Tasmanian devils. 

Elizabeth grew up in Tasmania, where she loved to catch glimpses of the island’s unique wildlife during hikes in the rugged wilderness. She obtained her undergraduate degree from the University of Melbourne, and performed doctoral research at Cold Spring Harbor Laboratory, New York. After a postdoctoral fellowship at the Wellcome Sanger Institute, where she sequenced the genome of the Tasmanian devil and its transmissible cancer, she joined the University of Cambridge in 2013. She is a keen science communicator and in 2011 she delivered a TED talk entitled Fighting a Contagious Cancer which has been translated into 29 languages and viewed by a global audience more than 500,000 times.

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.

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

Dr Bowling completed her PhD at Imperial College London in the labs of Tristan Rodriguez and Jesus Gil, where her project focused on understanding the mechanisms and roles of cell competition in early mouse development. For her postdoctoral research, she co-developed new mouse models that enable the simultaneous tracing of thousands of cells in vivo with unique, transcribed cellular barcodes. Using these models, she has mapped the origins of the hematopoietic system and created a blueprint of lineage decisions taken by cells during gastrulation. She will be starting her lab in the Developmental Biology Department at Stanford University School of Medicine in early 2024. Her laboratory will study mechanisms of plasticity and resilience in the mammalian embryo, and use this knowledge to extend our understanding of regeneration and disease.

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

Michael Ratz is a group leader at Karolinska Institute in Stockholm, Sweden. He started his lab in 2023 to study the molecular mechanisms of mammalian brain development in health and disease using cutting edge tools in molecular and synthetic biology, single-cell and spatial transcriptomics as well as computational biology.

Michael conducted postdoctoral research with Jonas Frisén (Karolinska Institute, Sweden) and Joakim Lundeberg (KTH, Sweden), where he pioneered the development of next-generation clonal tracing to reveal the developmental origins of the mammalian brain at the level of single cells. During his postdoc, Michael has also been a visiting researcher in the lab of Karl Deisseroth (Stanford University, USA) where he got acquainted with 3D intact-tissue RNA-sequencing.

Michael received a PhD in molecular biology from the University of Göttingen, where he worked in the labs of Stefan Jakobs and Stefan W. Hell at the Max Planck Institute for Biophysical Chemistry. 

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

Bushra Raj, PhD, is an Assistant Professor in the department of Cell and Developmental Biology at the University of Pennsylvania Perelman School of Medicine. Dr Raj obtained her PhD at the University of Toronto and completed her postdoctoral training at Harvard University. During her postdoc, Dr Raj developed a new technology that enables simultaneous readouts of cell identity and cell lineage relationships during zebrafish brain development at high throughput and with single-cell resolution. The Raj lab studies cell specification and gene regulatory programs underlying brain development using zebrafish as a model. Specifically, the Raj lab is developing novel genomics and CRISPR/Cas tools to investigate how Notch signaling, progenitor cell transcriptional identities and lineage histories coordinate cell fate decisions in the brain. Dr Raj is the recipient of a K99/R00 grant from NICHD and the DP2 New Innovator Award from NINDS.