Detlev Arendt, Ph.D. | EMBL Heidelberg

"Whole-body correlation of gene expression with single-cell morphology"

Abstract: We take advantage of the highly stereotypic development of the marine annelid Platynereis dumerilii to establish the link between gene expression and cellular ultrastructure for the entire larval body. To this end, we have spatially registered a high-resolution serial block-face electron microscopy dataset to a whole-body cellular gene expression atlas for 6dpf Platynereis. To analyze cellular morphology in detail we develop an automated segmentation pipeline that we use to render the somatic volume for all the cells in the organism. We also provide an integrated browser to easily explore, analyze and visualize these datasets.

Bio: Detlev Arendt studied biology at the University of Freiburg in Germany, where he also obtained his doctorate in natural sciences. His laboratory in the Developmental Biology Unit at the European Molecular Biology Laboratory has established the marine annelid Platynereis dumerilii as a molecular model for evolutionary, developmental and neurobiological research. His major interest is the evolution of animal body plans and nervous systems. He has also studied the evolution of photoreceptor cells and in recent years pioneered the new field of cell type evolution and development. He has been a senior scientist at EMBL since 2007, has received two consecutive European Research Council Advanced Grants since 2012; is a European Molecular Biology Organization member since 2015; and holds a honorary professorship at the Centre for Organismal Studies at Heidelberg University.

Connie Cepko, Ph.D. | Harvard Medical School/HHMI

"The relationships of lineage, birthdate, and birthplace in the murine retina"

Abstract: The retina provides a model of a complex tissue comprising approximately 100 neuronal and two glial cell types. These cell types have frequencies of .002-75%, and are approximately evenly distributed across the retina. The mechanisms that generate this diversity, frequency, and distribution are being investigated, using lineage studies, gene expression profiling, and cis-regulatory modules. We are currently focusing on one set of interneurons, the bipolar cells, comprising 15 different types. These cell types are being analyzed with respect to their clonal relationships, their birthplaces, their birthdays, and the timing of their fate determination.

Bio: Dr. Cepko is the Bullard Professor of Genetics and Neuroscience at Harvard Medical School and an Investigator of the Howard Hughes Medical Institute. She received her PhD degree from MIT, working with Phillip Sharp, and remained at MIT as a postdoctoral fellow in the laboratory of Richard Mulligan, where she developed some of the first retrovirus vectors. Her current research is focused on the development and diseases of the central nervous system, with an emphasis on the retina. Her laboratory uses molecular and cellular methods to address questions regarding the mechanisms of cell fate determination. They also have been developing gene therapy to prolong vision in genetic forms of blindness. In order to trace neurons that form circuits, they have developed viral vectors based upon VSV as a transsynaptic tracer. To enable the manipulation of specific cell types in vivo in model and non-model organisms, they have developed new tools based upon nanobodies. Dr. Cepko is a member of American Academy of Arts and Sciences and the National Academy of Sciences. She has launched and directed two PhD graduate programs, and is currently serving as the Co-Director of the Leder Human Biology and Translational Medicine Program.

Michelle Chan, Ph.D. | University of California, San Francisco

"Applications for lineage tracing in mouse embryogenesis"

Abstract: Understanding the emergence of complex multicellular organisms from single totipotent cells, or ontogenesis, represents a foundational question in biology. The study of mammalian development is particularly challenging due to the difficulty of monitoring embryos in utero, the variability of progenitor field sizes, and the indeterminate relationship between the generation of uncommitted progenitors and their progression to subsequent stages. We have made a high-information molecular recorder, and have previously applied it as a lineage tracer to chart the cell fate map for mouse embryogenesis. I will describe improvements to the molecular recorder including our efforts towards making the technology more accessible and reproducible.

Bio: Michelle Chan is a postdoc in Jonathan Weissman's group at UCSF. She completed her Ph.D. in Computational and Systems Biology at MIT in 2013.  Michelle’s research interests are in understanding the regulation that determines cell state with a focus in mammalian developmental biology.  Michelle’s graduate work characterized the dynamics of DNA methylation during mammalian pre-implantation development in mouse and human.  In her postdoc, Michelle developed a CRISPR-Cas9 based molecular recorder and applied it as a lineage tracer to mouse embryogenesis producing a cell fate map at single cell resolution. 

Lionel Christiaen, Ph.D. | New York University

"Regulatory states along cardiopharyngeal trajectories in chordates"

Abstract: During embryonic development, diverse cell fates are progressively determined as multipotent progenitors divide and their daughter cells chose specific identities. Therefore, multipotent progenitors must preserve a broad developmental potential while acquiring the competence to produce specific cell fates. In vertebrates and their closest relatives, the tunicates, derivatives of the second heart lineage share a common origin with head/pharyngeal muscle in the cardiopharyngeal mesoderm. I will first present extensive characterizations of the dynamic gene expression programs and chromatin accessibility profiles underlying early cardiopharyngeal fate choices. Remarkably, cell fate choices appear to be coupled with stereotyped divisions, permitting the emergence of diverse cardiac and pharyngeal muscle identities. An experimental approach combining transgene-based sample barcodes and single cell transcriptomics to analyze multipotent cardiopharyngeal progenitors collected at ten time points revealed gene expression dynamics and successive regulatory states through which cells transition collective migration within one interphase. We refer to this dynamic as multipotent progenitor maturation, and surmise that it underlies the acquisition of cardiopharyngeal competence. Finally, I will discuss progress incorporating single cell transcriptomics, chromatin accessibility, and CRISPR/Cas9-mediated perturbations into gene regulatory network models for cardiopharyngeal multipotency, competence and early fate choices.  

Bio: A French citizen, Pr. Christiaen obtain his BS from the Ecole Normale Supérieure in Paris. He obtained is PhD from the University of Paris XI in 2004, working under the supervision of Dr. Jean-Stéphane Joly, using the tunicate Ciona and evo-devo methods to study the evolutionary origins of the vertebrate mouth and pituitary gland. From 2005 to 2009, As a postdoc with Pr. Mike Levine, at UC Berkeley, he developed methods to profile the transcriptome of multipotent cardiopharyngeal progenitors using FACS and microarrays, and characterized the transcription-migration interface in Ciona embryos. An assistant (2009-2015), and now associate professor of Biology at New York University, he continued to characterize cardiopharyngeal development in chordates, with a special focus on the tunicate Ciona, combining genomics, systems biology and cell biology, to learn general principles about the regulatory mechanisms governing multipotency, fate choices and cell behaviors in developing embryos. 

George Church, Ph.D. | Harvard University

"De novo & targeted in situ sequencing of biomolecules & lineage"

Abstract: Lineage recording in DNA is one of the better working examples of polymer storage of information —roughly a terabyte per mouse (time-series data potentially over months).  This can be generalized to storing other a few specific targets in living organisms and then integrated with dense DNA, RNA and protein data at subcellular resolutions ranging down to 20 nm and thicknesses up to 100 microns.  Proteins, barcodes and high resolution are particularly valuable when assessing interactions among cells such as synapses and non-synpatic peptide signaling.

Bio: George M. Church, PhD ’84, is professor of genetics at Harvard Medical School, a founding member of the Wyss Institute, and director of, the world’s only open-access information on human genomic, environmental, and trait data. Church is known for pioneering the fields of personal genomics and synthetic biology. He developed the first methods for the first genome sequence & dramatic cost reductions since then (down from $3 billion to $600), contributing to nearly all “next generation sequencing” methods and companies. His team invented CRISPR for human stem cell genome editing and other synthetic biology technologies and applications – including new ways to create organs for transplantation, gene therapies for aging reversal, and gene drives to eliminate Lyme Disease and Malaria.  Church is director of IARPA & NIH BRAIN Projects and National Institutes of Health Center for Excellence in Genomic Science.  He has co-authored more than 515 papers and 130 patent publications, and one book, “Regenesis”. His honors include Franklin Bower Laureate for Achievement in Science, the Time 100, and election to the National Academies of Sciences and Engineering. 

Jan Huisken, Ph.D. | Morgridge Institute for Research

"Towards a cellular blueprint of vertebrate development with custom light sheet microscopy"

Abstract: Light sheet microscopy allows us to image living organisms at high resolution and in toto with its low photo-toxicity and fast acquisition. However, visualizing the interplay of all tissues simultaneously across an entire embryo requires multi-view, multi-color, three-dimensional time-lapse imaging and analysis. Custom microscope hardware and software is needed to streamline acquisition and real-time data processing to avoid superfluous data. We combine fast long-term imaging with single cell resolution across the entire embryo, a multi-scale computational analysis framework based on single-cell tracking and the interactive, web-based visualization of the data to study different aspects of development in vertebrates.

Bio: Jan Huisken is a principal investigator and director of Medical Engineering at the Morgridge Institute for Research and Professor at the University of Wisconsin-Madison. Jan studied physics in Göttingen and Heidelberg and has a background in three-dimensional fluorescence microscopy, optical manipulation and trapping, developmental biology and zebrafish development. He received his PhD from the EMBL Heidelberg, where he pioneered multidimensional light sheet microscopy (also Selective Plane Illumination Microscopy, SPIM) in the labs of Ernst Stelzer and Joachim Wittbrodt. For one of the first applications of light sheet microscopy, Huisken moved to the lab of Didier Stainier at the University of California, San Francisco as a cross-disciplinary HFSP postdoctoral fellow in 2005 to study cardiovascular morphogenesis and function in zebrafish. From 2010 until 2016 Huisken was an independent group leader at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden, Germany. Huisken is now best known for his interdisciplinary work at the interface of gentle high-resolution microscopy and quantitative developmental biology. His lab covers all aspects of modern in vivo imaging from sample preparation to image analysis. Recently he has started an initiative to democratize the access to advanced microscopy with a modular and portable microscope platform called Flamingo. For his contributions to modern optical microscopy Huisken was awarded the Royal Microscopy Society Medal for Light Microscopy in 2017.

Celina Juliano, Ph.D. | University of California, Davis

"Stem cell differentiation trajectories in Hydra resolved at single cell resolution"

Abstract: The adult Hydra continually renews all cells using three distinct stem cell populations. We sequenced approximately 25,000 Hydra cells and identified the molecular signatures of cell states, from stem cells to terminally differentiated cells. We constructed differentiation trajectories for each lineage and identified the transcription factors expressed along these trajectories, thus creating a multi-lineage map of an adult organism. Altogether, we have built a comprehensive molecular description of Hydra homeostatic development. We are currently using single cell sequencing to test the effect of manipulating signaling pathways on Hydra stem cell differentiation pathways.

Bio: Dr. Juliano joined the faculty at UC Davis in 2015 as an Assistant Professor in the Molecular and Cellular Biology Department. She is a developmental biologist with a long-standing interest in stem cell biology. Her doctoral research, mentored by Dr. Gary Wessel at Brown University, focused on understanding the molecular mechanisms underlying the maintenance of plasticity during sea urchin development. Dr. Juliano completed her post-doctoral work at Yale University in the laboratory of Dr. Haifan Lin with co-mentoring from Dr. Rob Steele at UC Irvine. At Yale, Dr. Juliano began working with Hydra, a small freshwater cnidarian that continually renews all cell types as an adult and has remarkable regenerative abilities. During her post-doctoral work, she discovered a critical role for the PIWI-piRNA pathway in Hydra stem cells. In her own laboratory at UC Davis, Dr. Juliano continues to use Hydra as a model to understand stem cell function, development, and regeneration. In her most recent publication, Juliano and her team subjected the adult Hydra to single cell sequencing, created a molecular map of the entire organism, and built differentiation trajectories to describe each stem cell differentiation pathway. This work now serves as a foundation for her laboratory’s current research goals, which include dissecting the molecular mechanisms underlying stem cell differentiation, understanding how the conserved injury program triggers developmental pathways during regeneration, and understanding how the Hydra nervous system is able to continually remove and add neurons into neural circuits. 

Jan Philipp Junker, Ph.D. | Max Delbrück Center for Molecular Medicine

"Cellular drivers of injury response and regeneration in the zebrafish heart"

Abstract: We recently developed LINNAEUS, a CRISPR/Cas9-based method for simultaneous transcriptome profiling and lineage tracing of thousands of single cells. Here, we introduce experimental and computational improvements of the approach, including strategies for increasing the number of target sites for lineage recording, and methods for integrating lineage data across individual organisms.  CRISPR/Cas9 lineage tracing has so far mainly been used during embryonic development. We will present an unpublished study in which we now apply LINNAEUS to study regeneration of the adult zebrafish heart in order to identify the origin and function of transient cell types that are generated upon injury. 

Bio: Philipp Junker is a research group leader at the Max Delbrueck Center in Berlin. He received his PhD in biophysics from Technische Universitaet Muenchen, which included the first direct observation of mechanically observed single protein folding/unfolding transitions in thermodynamic equilibrium. In his postdoctoral work in Alexander van Oudenaarden’s group (at MIT and at the Hubrecht Institute, Utrecht), he investigated gene regulatory mechanisms of robustness in developmental patterning, and he developed the tomo-seq method for spatially resolved transcriptomics in 3D. Using the zebrafish as their primary model system, his group develops novel methods for high-throughput lineage tracing using CRISPR/Cas9 technology. The main goal of the lab is to understand naturally occurring variability in vertebrate development and its relationship to robustness to variation. Philipp Junker obtained an ERC Starting Grant, received the Minerva ARCHES award for German-Israeli collaboration, and was selected as an EMBO Young Investigator. 

Tzumin Lee, Ph.D. | HHMI Janelia Research Campus

"Tracking genesis of neuron diversity by dynamic developmental recording"

Abstract: Complex neural networks consist of many neurons with distinct identities. Important aspects of neuronal identity include which genes are expressed (transcriptome), the cell’s shape (morphology) and its connection to other neurons (connectome). A majority of these features are generated during development. In the Drosophila brain, we have shown that neural stem cells produce morphologically distinct neurons in an invariant order. Lineage mapping, together with genetic mosaic molecular studies, indicate that neuronal diversity is generated by a series of fating events, including lineage, temporal and binary sister fate specification. We are now working toward incorporating single-cell transcriptomics with lineage tracing, by using dynamic developmental recording. We begin with lineages that have been morphologically mapped at a high temporal resolution. We ultimately strive to build a genome-to-connectome brain map.

Bio: Tzumin Lee earned his PhD at Johns Hopkins Medical School where he acquired the power of Drosophila genetics from Dr. Denise Montell. He then studied the development of the nervous system in Liqun Luo’s lab at Stanford. Lee set out to develop a way to label specific neurons based on cell lineage. The technique, called mosaic analysis with a repressible cell marker, or MARCM, is used to discover the functions of genes, as well as trace the lineages of neurons and the paths of neural impulses. Besides uncovering genes critical for lineage-guided neural development, Lee has taken MARCM further, creating twin-spot MARCM and lineage-restricted genetic drivers. These refinements make it easier to identify individual neurons and their origins. At Janelia, Lee aims to reconstruct the development of the fruit fly brain at both cellular and molecular levels and extend similar analyses to higher brains.

Prisca Liberali, Ph.D. | Friedrich Miescher Institute for Biomedical Research

"Regenerative landscape of intestinal organoids"

Abstract: Development of intestinal organoids from single intestinal stem cells recapitulates the regenerative capacity of the intestinal epithelium. To unravel molecular mechanisms orchestrating organoid formation and regeneration of intestinal tissue, we follow organoids with single cell tracking trough their full development with custom built light-sheet microscopes and delineate the mechanisms underlying their self-organization and symmetry breaking. We then will present the morphogenesis of crypt formation while single cells acquire their identity. Our findings reveal how single cells exposed to a uniform growth-promoting environment have the intrinsic ability to generate emergent, self-organized behavior resulting in the formation of complex multicellular asymmetric structures.

Bio: Prisca Liberali has been trained as physical organic chemist with a focus on physical organic chemical reactions. During her postdoc, she developed new experimental single-cell methods and statistical approaches to analyse and model cell-to-cell variability and its involvement in the emergence of complex cellular populations. Currently, she is an assistant professor at the University of Basel and at the Friedrich Miescher Institute for Biomedical Research (FMI) with a laboratory focused on dynamics of self-organization and on how cellular signalling dictates its spatial-temporal regulation. To address this in a fully tractable experimental model system that mimics conditions of tissue formation in organisms, her laboratory uses stem cells derived organoids and gastruloids. As these emergent systems have multiple layers of biological organization at different scales, her laboratory is developing novel image-based experimental, and statistical methods to increase our integrated understanding of single-cell biology. Prisca Liberali has received several research awards, including an ERC Starting Grant (2018-2022) and a SNSF Professorship Grant (2015-2021). 

Carlos Lois, Ph.D. | California Institute of Technology

"Lineage-independent synaptic connectivity and its role in brain circuit resilience"

Abstract: Brain function is remarkably reliable despite the continuous perturbations caused by aging, disease or injury. How does the brain manage to produce stereotypic behaviors over long periods of time and adapt to these perturbations? To study the cellular mechanisms of brain resilience we have focused on the mouse olfactory system. Despite the crystalline structure of its connectivity, lineage does not determine the organization of the synaptic inputs into the olfactory bulb. In addition, olfactory function persists after the selective genetic ablation of more than 95% of cells of an essential olfactory bulb neuronal type. These observations suggest that decoupling cell lineage from synaptic connectivity may enable long-term resilience of brain function.

Bio: Carlos Lois is a Research Professor in Neurobiology at the Division of Biology and Biological Engineering at Caltech. Dr. Lois' PhD work demonstrated that the subventricular zone in the brain of adult mice contains stem cells that move long distances through the brain and differentiate into neurons in the olfactory bulb, via a new form of migration that is now known as neuronal chain migration. As a postdoctoral fellow he developed lentiviral transgenesis, an effective method that is now widely used to genetically manipulate animal species that were previously refractory to germline molecular manipulations, such as birds and non-human primates. The Lois lab currently focuses on the generation of neuronal diversity and assembly of neuronal circuit assembly during postnatal neurogenesis. To address these questions his laboratory develops new methods to genetically manipulate the development and biophysical properties of neurons. Honors include the Ellison Foundation New Scholar award, the Packard Foundation Scholar award, and two NIH BRAIN initiative awards. He received his MD from the University of Valencia (Spain), his PhD in neurobiology from The Rockefeller University in 1995, and did postdoctoral work at MIT and Caltech.  

Rong Lu, Ph.D. | University of Southern California

"Learning from the heterogeneity of hematopoietic stem cell differentiation and leukemia progression in vivo"

Abstract: Tracking disparate cellular activities and the associated molecular differences can reveal new mechanisms underlying stem cells and cancer. Using a lentivirus based genetic barcoding and single cell mRNA sequencing system, we show that the heterogeneous differentiation of mouse hematopoietic stem cells (HSCs) is cell autonomous and associated with distinct gene expression dynamics. Some HSC clones change their differentiation programs during aging and develop a lymphoid deficiency that is associated with reduced life spans in mice. We also show how individual human leukemia cell clones differentially expand, migrate and respond to various chemotherapies in a patient-derived xenograft model.

Bio: Dr. Rong Lu is the Richard N. Merkin Assistant Professor of Stem Cell Biology and Regenerative Medicine, Biomedical Engineering, Medicine, and Gerontology at USC (tenure-track). Her lab studies hematopoietic stem cell (HSC) regulation, coordination and malfunction using systems biology and single-cell approaches. Dr. Lu has been an active researcher in the stem cell field for the past sixteen years. She received her Ph.D. training in molecular biology under the guidance of Dr. Ihor R. Lemischka at Princeton University. At Princeton, she developed innovative systems biology approaches to determine the coordination between the epigenome, the transcriptome, and the proteome during embryonic stem cell differentiation. Later, she received her postdoctoral training in cell biology under the mentorship of Dr. Irving L. Weissman at Stanford University. At Stanford, she developed an innovative cellular tracking technology with single-cell sensitivity and high-throughput capacity using genetic barcoding and next generation sequencing. She made the first direct measurement of in vivo HSC differentiation at the clonal level through multiple stages of lineage commitment. This technology has now been adopted by many research labs. After starting her own lab at USC in 2014, Dr. Lu has further advanced her cellular tracking technology by integrating it with single cell RNA-seq and single cell ATAC-seq techniques. With the new technical advances, she is now studying the mechanisms underlying differences between individual HSCs, and the coordination between their differentiations. She is also investigating the heterogeneity of primary human leukemia cells, including their individual chemo responses.  

Liqun Luo, Ph.D. | Stanford University/HHMI

"Exploring the relationship between lineage, birth timing, connectivity, and function of cerebellar granule cells"

Abstract: Cerebellar granule cells comprise over half of all neurons in the mammalian brain, yet no stable transcriptomically defined subtypes have emerged. Our previous MADM-based mosaic analysis revealed that granule cells derived from the same progenitor are born within a narrow time window and project axons to a limited sub-layer of the cerebellar cortex (Zong et al., 2005; Espinosa and Luo, 2009). We recently developed genetic strategies to access early- and late-born granule cells and are comparing their mono-synaptic inputs and physiological properties in behavioral paradigms that assess sensorimotor and cognitive functions (Wagner et al., 2017; 2019).

Bio: Dr. Luo grew up in Shanghai, China, and earned his bachelor's degree from the University of Science & Technology of China. After receiving his PhD at Brandeis University and postdoctoral training at UCSF, Dr. Luo started his own lab at Stanford University in 1996. Together with his postdoctoral fellows and graduate students, Dr. Luo studies the development and function of neural circuits in fruit flies and mice. Dr. Luo is currently the Ann and Bill Swindells Professor of Humanities and Sciences, Professor of Biology, and Professor of Neurobiology by courtesy, all at Stanford University. He is also an Investigator of the Howard Hughes Medical Institute. He teaches neurobiology to undergraduate and graduate students. His single-author textbook Principles of Neurobiology (Garland Science 2015) is widely used for undergraduate and graduate courses across the world. Dr. Luo is a recipient of the McKnight Technological Innovation in Neuroscience Award, the Society for Neuroscience Young Investigator Award, the Jacob Javits Award from National Institute of Neurological Disorders and Stroke, HW Mossman Award from American Association of Anatomists, the Lawrence Katz Prize from Duke University, and the Pradel Research Award from the National Academy of Sciences. Dr. Luo is a Member of the National Academy of Sciences and a Fellow of the American Academy of Arts and Sciences. 

John Marioni, Ph.D. | EMBL - European Bioinformatics Institute

"Modelling early mammalian development using single cell approaches"

Abstract: Technical advances have allowed cellular decision making processes to be probed, genome wide, at single cell resolution. In this presentation, I will discuss how we have used a variety of high-throughput tools to profile decision making during mouse gastrulation. I will show how reference atlases, in conjunction with appropriate perturbations, can provide novel insights into how transcriptional changes are regulated and how this impacts early development.

Bio: John Marioni is a Research Group Leader at the EMBL-European Bioinformatics Institute, a Senior Group Leader at the CRUK Cambridge Institute within the University of Cambridge and an Associate Faculty member of the Wellcome Sanger Institute. John read for his PhD at the University of Cambridge under the supervision of Professor Simon Tavaré before becoming a postdoctoral scholar under the supervision of Professor Matthew Stephens at the University of Chicago. John’s lab has pioneered the development of methods for the analysis of single-cell genomics data. Subsequently, his lab has applied them, in conjunction with outstanding experimental collaborators, to understand cell fate decisions in early mammalian development. Complete list of Published Work in MyBibliography.

Rob Mitra, Ph.D. | Washington University School of Medicine

"Simultaneous analysis of transcription factor binding and mRNA expression in single cells"

Abstract: We have developed a novel single-cell ‘Calling Card’ (scCC) technology that can record genome-wide interactions of any DNA-binding protein (DBP), creating a permanent molecular memory of all binding events that occur at a given moment or epoch. Importantly, we have adapted this technology to the 10X Chromium platform so that DBP binding and mRNA transcriptomes can be simultaneously read out from single cells. Here, we demonstrate that scCC can faithfully map the binding of transcription factors in single cells in culture and in vivo.

Bio: Dr. Rob Mitra is the Alvin Goldfarb Professor of Computational Biology at the Washington University School of Medicine in St. Louis.  Dr. Mitra received his BS, MS and PhD from MIT.  He trained with George Church where he did some of the earliest work developing 2nd generation sequencing technologies.  His lab in the Genetics Department and Center for Genome Sciences and Systems Biology has continued to focus on genomic technology development and has pioneered novel methods for the analysis of transcription factor binding, single molecule proteomics, single-cell genomics, and the capture of targeted genomic regions.  His lab is interested in understanding how transcription factors achieve their in vivo binding specificities, the  impact of this binding on transcriptional output, and the role that transcription factors and chromatin modifiers play in neurodevelopment.  Dr. Mitra played integral parts in the founding of the Center for Genome Sciences DNA Sequencing Innovation Lab, the Washington University Genomic Technology Access Center (GTAC@MGI), the Washington University Genomics and Pathology Services Lab (GPS@WU), and the Genome Engineering and iPSC Core (GEiC@MGI).

Samantha Morris, Ph.D. | Washington University in St. Louis

"Single-cell recording of lineage and transcriptional regulation in direct reprogramming"

Abstract: Considerable heterogeneity arises during cellular reprogramming. We previously developed a straightforward, high-throughput cell tracking method, ‘CellTagging,’ that permits the construction of multi-level lineage trees. CellTagging and longitudinal tracking of fibroblast to induced endoderm progenitor reprogramming revealed two distinct trajectories: one leading to successfully reprogrammed cells, and one leading to a ‘dead-end’ state. Here, I present two new methods: one an experimental method to record transcription factor binding early in reprogramming, revealing trajectory-specific gene regulation; the second is a computational method to dissect gene regulatory network reconfiguration during reprogramming. Together, these tools provide new mechanistic insights into the reprogramming process.

Bio: Dr. Samantha Morris, Ph.D., is an Assistant Professor of Genetics and Developmental Biology at Washington University in St. Louis. Her laboratory studies the mechanisms of cell reprogramming, focusing on how pioneer transcription factors drive gene expression, epigenetic, and functional changes in cell identity. To enable these studies, her group develops novel, open-source single-cell experimental and computational approaches to longitudinally record lineage and gene regulation during directed reprogramming. With her team, Dr. Morris aims to engineer clinically relevant cell populations, translating new insights in cell fate specification into better models of disease and development. With clinical collaborators, her laboratory uses their genomic technologies to dissect mechanisms of pediatric gastrointestinal disease, such as Short Gut Syndrome and Hirschsprung’s Disease, with a long-term goal of developing novel regenerative therapies. Dr. Morris trained as a Developmental Biologist at the University of Cambridge. In Magdalena Zernicka-Goetz's group, she investigated mechanisms of cell fate decision-making in the earliest stages of development. She then joined the laboratory of George Daley at Harvard Medical School, where she focused on the analysis of gene regulatory networks to dissect and engineer cell identity. In 2015, she established her independent research group. In 2017, Dr. Morris was named a Vallee Foundation Scholar. In 2019, she was awarded the St. Louis Academy of Science Innovation Award and was named an Allen Distinguished Investigator. She sits on the Board of Directors of the Society for Developmental Biology and serves on the editorial boards of Development, Cell Systems, and Developmental Cell. 

Dana Pe'er, Ph.D. | Sloan Kettering Institute

"Mapping the emergence of organ identities in time & space"

Abstract: In this talk we will present approaches to infer trajectories from single-cell data. We present Palantir, an algorithm that infers trajectories of differentiating cells by treating cell fate as a probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Palantir generates a high-resolution pseudo-time ordering of cells and, for each cell state, assigns a probability of differentiating into each terminal state. We apply our algorithm to mouse embryo endoderm populations until midgestation. We characterize the transcriptional architecture that accompanies the emergence of the first (primitive or extra-embryonic) endodermal population and its sister pluripotent (embryonic) epiblast lineage. We uncover a relationship between descendants of these two lineages, in which epiblast cells differentiate into endoderm at two distinct time points-before and during gastrulation. Trajectories of endoderm cells were mapped as they acquired embryonic versus extra-embryonic fates and as they spatially converged within the nascent gut endoderm, which revealed these cells to be globally similar but retain aspects of their lineage history. We also present ATAC-velocity and demonstrate that incorporating ATAC-seq can both direct trajectories in the correct direction and also highlight the underlying regulators of this process. 

Bio: Dr. Dana Pe'er is the Alan and Sandra Gerry endowed chair, Chair of Computational and Systems Biology program, Director of the Alan and Sandra Gerry Center for Metastasis and Tumor Ecosystems and Director of SKI Single Cell Research Initiative. The Pe’er lab combines single cell technologies, genomic datasets and machine learning techniques to address fundamental questions addressing development, tumor heterogeneity, tumor plasticity, tumor immune interaction and metastatic transition, regulatory network functionand how this is derailed in disease. To answer these and additional key questions in biomedicine, Dana has taken a leadership role in the Human Cell Atlas project, to characterize all cells in the human body, how they organize into tissues and how these function in health and disease. Dana is recipient of the Burroughs Welcome Fund Career Award, NIH Director’s New Innovator Award, NSF CAREER award, Stand Up To Cancer Innovative Research Grant, Packard Fellow in Science and Engineering, Overton award, NIH Director’s Pioneer and Lenfest Distinguished Faculty Award.  

Kristy Red-Horse, Ph.D. | Stanford University

"Do alternative developmental trajectories influence adult cellular responses?"

Abstract: We typically envision cell fate trajectories during development as being linear pathways where a cell progressively differentiates into its final fate. However, modern lineage tracing has revealed that a seemingly homogeneous cell population is frequently comprised of cells that took very different developmental paths. Our long-term goal is to discover whether cells remember differential developmental trajectories on the molecular level into adulthood and whether this history influences tissue homeostasis, injury, and disease. Here, I will discuss how “different roads sometimes lead to the same castle” during heart development and our progress on understanding how alternative trajectories might affect heart function and regeneration.

Bio: Kristy Red-Horse is an Associate Professor in the Department of Biology at Stanford University. Dr. Red-Horse's laboratory uses cardiovascular development as a model to study the signals that instruct cell fate and guide morphogenesis during organ formation in the mammalian embryo. The current focus of the lab is to fate-map the different cellular sources that give rise to the coronary arteries of the heart and to identify the molecules that direct their migration and differentiation. The long-term goal is to use this information to better understand and treat cardiovascular diseases. Dr. Red-Horse received her PhD from the University of California, San Francisco and was a Postdoctoral Fellow at Genentech, Inc. and Stanford University. Honors include New York Stem Cell Foundation Robertson Investigator, Terman Fellow, Searle Scholar and Brown Faculty Fellow.

Ellen Rothenberg, Ph.D. | California Institute of Technology

"Mechanisms accounting for real-time dynamics of lineage determination in early T-cell development"

Abstract: The early stages of T-cell development in the thymus are a highly accessible, tractable system in which the transition from multipotentiality to lineage commitment can be tracked in real time in single cells and dissected by perturbations.  Single-cell transcriptome analysis has clarified how transcription factor gene expression changes predict developmental potential changes within individual cells. Driving these changes is a T-cell specification gene regulatory network activated by Notch signaling.  However, this network is opposed both by an inertial drag of epigenetic repression and by an actively opposing progenitor-cell gene regulatory network. These are resolved as discussed in the talk. 

Bio: Ellen Rothenberg is the Albert Billings Ruddock Professor of Biology at the California Institute of Technology, Pasadena, CA, USAHer group’s research is at the interface of immunology, stem cell developmental biology, systems biology, and genomics. She received her bachelor's degree in Biochemical Sciences from Harvard University and her Ph.D. from Massachusetts Institute of Technology. After a Jane Coffin Childs Postdoctoral Fellowship at Sloan-Kettering Institute and an Assistant Research Professorship at The Salk Institute, she came to Caltech in 1982 and rose to become Albert Billings Ruddock Professor in 2007. She was elected Fellow of the American Association for the Advancement of Science in 2017, Fellow of the American Academy of Arts and Sciences in 2018, and a member of the inaugural class of Distinguished Fellows of the American Association of Immunologists in 2019. She won the Richard P. Feynman Prize for Excellence in Teaching in 2016 and eight other teaching awards (1988-2014) at Caltech, and has taught internationally on immunology, developmental biology, and gene regulatory networks.  She has organized multiple international conferences in immunology and systems biology and has served on Scientific Advisory Boards for US and international research institutes, Editorial Boards of several immunology journals, committees for the American Association of Immunologists, and grant review panels for NIH, NASA and private foundations. She studies gene regulation and development of T lymphocytes, gene networks controlling hematopoietic cell fates, and mechanisms underlying the dynamics of single-cell developmental decisions. 

Rahul Satija, Ph.D. | New York Genome Center

"Integrated analysis of single-cell data across technologies and modalities"

Abstract: Massively parallel, multi-modal technologies represent an exciting opportunity to move beyond the transcriptome, and explore how multiple aspects of cellular identity define behavior and function. We introduce a new computational framework ‘weighted-nearest neighbor’ analysis, that learns the relative information content of each modality in each cell, and constructs a joint neighbor graph that integrates the complementary data types together. When applied to a CITE-seq dataset simultaneously profiling cellular transcriptomes and hundreds of surface proteins, our work characterizes the extensive multimodal heterogeneity in human blood, and demonstrates the necessity of defining cellular states from multiple perspectives.

Bio: Rahul Satija, PhD, is a Core Member and Assistant Investigator at the New York Genome Center, with a joint appointment as Assistant Professor at Center for Genomics and Systems Biology at NYU. Dr. Satija’s group focuses on developing computational and experimental methods to sequence and interpret the molecular contents of a single cell. His group applies single cell genomics to understand the causes and consequences of cell-to-cell variation, with a particular focus on immune regulation and early development. His group has developed and maintained the R package Seurat for the analysis, exploration, and integration of single-cell data. Dr. Satija holds a BS in Biology and Music from Duke University, and obtained his PhD in Statistics from Oxford University as a Rhodes Scholar. Prior to joining NYGC, he was a postdoctoral researcher at the Broad Institute of Harvard and MIT, where he developed new methods for single cell analysis.

Alex Schier, Ph.D. | Biozentrum Basel

Keynote: "Reconstructing Cellular Biographies: Insights from Zebrafish"

Abstract: Complex gene expression programs determine the biographies of cells: how a cell divides, becomes specialized and differentiates. I will describe our recent efforts to use single-cell RNA sequencing and CRISPR-Cas9 genome editing to generate new tools to reconstruct differentiation trajectories and lineage trees at very large scales. Using mesoderm and brain development as examples, I will discuss the opportunities and challenges for these technologies to reveal the developmental biology of cells (also see McKenna et al. Science 2016; Farrell et al. Science 2018; Raj et al. Nature Biotechnology 2018; Raj et al. Biorxiv 2019).

Bio: Alex Schier obtained his PhD from the Biocenter in Basel, Switzerland, where he studied the transcriptional regulation of homeobox genes in Walter Gehring's lab. He spent his postdoc in Wolfgang Driever's lab in Boston, where he screened for and characterized mutants affecting zebrafish development. He started his lab in 1996 at the Skirball Institute of the New York University School of Medicine and joined Harvard University in 2005, where is the Leo Erikson Life Sciences Professor of Molecular and Cellular Biology and Chair of the Department of Molecular and Cellular Biology. Dr. Schier’s lab has contributed to the understanding of the molecular basis of embryogenesis and behavior and to the development of zebrafish as a model system. Dr. Schier was a McKnight Scholar for Neuroscience, an Irma T. Hirschl Scholar, and an Established Investigator of the American Heart Association and received the Harland Winfield Mossman Developmental Biologists Award of the American Association of Anatomists and the Everett Mendelsohn Award for Excellence in Graduate Student Mentoring. He received a NIH MERIT award in 2016. Members of his lab have gone on to PI positions at leading institutions, including Princeton, Caltech, UCLA, University of Toronto, Yale, NYU School of Medicine, University College London, MPI Dresden, UCSD, IMP Vienna, and MPI Tuebingen.

Cole Trapnell, Ph.D. | University of Washington

"Massively multiplex chemical transcriptomics at single cell resolution"

Abstract: High-throughput chemical screens typically employ coarse assays, e.g. cell survival, limiting what can be learned about mechanisms of action, off-target effects, and heterogeneous responses. Here we introduce sci-Plex, which uses ‘nuclear hashing’ to quantify global transcriptional responses to thousands of independent perturbations at single-cell resolution. As a proof-of-concept, we applied sci-Plex to screen 3 cancer cell lines exposed to 188 compounds. In total, we profiled ~650,000 single-cell transcriptomes across ~5,000 independent samples in one experiment. Our results reveal substantial intercellular heterogeneity in response to specific compounds, commonalities in response to families of compounds, and insight into differential properties within families. In particular, our results with HDAC inhibitors support the view that chromatin acts as an important reservoir of acetate in cancer cells.

Bio: Cole Trapnell is an Associate Professor of Genome Sciences at the University of Washington. Dr. Trapnell has formal training in both computational and experimental biology, with a broad background in functional genomics and specific training in next generation sequencing and gene expression analysis.  As a graduate student with Steven Salzberg and Lior Pachter, Dr. Trapnell wrote TopHat and Cufflinks, two widely used tools for transcriptome sequencing (RNA-seq) analysis. As a postdoctoral fellow in John Rinn's lab at Harvard, Dr. Trapnell sought experimental training focused on analysis of cell differentiation, and developed “single-cell trajectory analysis”, an approach for studying cell differentiation using single-cell RNA-seq. At the University of Washington, the Trapnell lab develops single-cell genomics assays and the algorithms needed to analyze them. The lab then applies these technologies to dissect the genetic architecture that governs cell fate decisions in development, reprogramming, and disease. The Trapnell lab co-developed, along with Jay Shendure’s lab, a general, ultra-scalable workflow for single-cell genomics called “combinatorial cellular indexing”. They recently used this approach to construct a transcriptional atlas for the C. elegans nematode and profile organogenesis in the mouse at whole-embryo scale. Dr. Trapnell was the recipient of an NIH Director's New Innovator Award, an Alfred P. Sloan Fellowship, the Dale F. Frey Award, and the ISCB Overton Prize.

Christopher A. Walsh, M.D., Ph.D. | Harvard Medical School

"Cell lineage in the human cerebral cortex using somatic mutations and RNA analysis"

Abstract: The cerebral cortex undergoes massive expansion in the primate lineage, especially in humans, but very little information is available on patterns of cell proliferation and lineage outside of rodents. Direct knowledge of cell lineage in human brain is especially important because of the role of somatic mutations in brain cancer and in an increasingly wide array of other neurological diseases including epilepsy and autism spectrum disorders. We have shown that newborn neurons in human cerebral cortex already show hundreds of somatic single nucleotide variants (SNV) relative to the germline, in addition to clonal retrotransposon insertions, microsatellite mutations, and copy number variants (CNV).  Somatic SNV occur frequently with each cell division, 2-3 SNV/genome/cell division, providing in principle enough information to provide a permanent, systematic, forensic lineage map of the brain of any species. Recent work combines single-cell DNA sequencing and bulk sequencing to identify clonal somatic mutations, and then adds RNA analysis to assess neuronal and glial cell types.   

Patterns of lineage in human cerebral cortex show some similarities to rodent, with early divergence of excitatory and inhibitory lineages, and widespread dispersion of interneuron clones.  Somatic SNV also allow the demonstration that excitatory neurons in deep cortical layers become postmitotic before upper layer neurons.  But human cell lineage shows marked widespread dispersion and intermingling of clonally related neurons even in the excitatory lineage at low levels of mosaicism.  Each cortical unit is composed of neurons derived from multiple progenitors distinct from early stages, and functionally cortical borders are only respected by clones that make up <3% of cells.  These results have important consequences for clonal patterns of distribution of disease-associated mutations that confer risk to neuropsychiatric disease.  Supported by the NIMH, NINDS, The Paul G. Allen Frontiers Group, and HHMI. 

Bio: Christopher A. Walsh is Bullard Professor of Pediatrics and Neurology at Harvard Medical School, Chief of the Division of Genetics and Genomics at Boston Children's Hospital, and an Investigator of the Howard Hughes Medical Institute. Dr. Walsh completed his MD and PhD degrees at the University of Chicago, neurology residency and chief residency at Massachusetts General Hospital, and postdoctoral training in Genetics at Harvard Medical School with Dr. Connie Cepko.  In 1993 he became Assistant Professor of Neurology at Harvard and Beth Israel Deaconess Medical Center. From 2003-2007 he served as Director of the Harvard-MIT Combined MD-PhD training program. He moved to Boston Children’s Hospital in 2006, becoming Chief of Genetics. Dr. Walsh’s research has focused on the development, function, and evolution and of the human cerebral cortex, pioneering the analysis of genetic diseases that affect the developing brain, and has discovered that some of these disease genes were important targets of the evolutionary processes that shaped the human brain.  In 2017 he inaugurated the Allen Discovery Center for Human Brain Evolution at Boston Children’s Hospital and Harvard Medical School, bringing together brain science with evolutionary genetics to search for the key changes in the genome that endow humans with their unique abilities for language, art, culture, and science. Dr. Walsh is an elected member of the American Association of Physicians, the American Association for the Advancement of Sciences, the National Academy of Medicine, the American Academy of Arts and Sciences, and the National Academy of Sciences. 

Bob Waterston, Ph.D. | University of Washington

"Transcriptome profiling with lineage and single cell resolution in Caenorhabditis"

Abstract: Single cell RNA-seq of the developing C. elegans embryo revealed the expression changes from gastrulation to terminal cell differentiation (Packer et al., Science, 2019) of more than 110 terminal cell types.  We have since extended the analysis to additional life stages, with the overall goal of delineating the transcriptome profile of the complete life cycle.  In addition we have begun a comparative analysis, using C. briggsae, which has a nearly identical embryonic cell lineage, despite its extensive evolutionary divergence.

Bio: Robert H. Waterston is a Professor and former William Gates III chair of Genome Sciences at the University of Washington. He partnered with John Sulston in pioneering whole genome analysis, first with the construction of the physical map of the C. elegans genome and later with sequencing the worm, human and other genomes. He also joined with Sulston to advocate for the rapid, unconstrained release of the sequence. He was educated at Princeton University (BSE) and the University of Chicago (MD/PhD) and interned at Children’s Hospital in Boston. After his postdoctoral fellowship at the MRC Laboratory of Molecular Biology with Sydney Brenner, where he first met Sulston, he joined the faculty at Washington University St. Louis. He moved to the University of Washington in 2002 as the founding chair of the Department of Genome Sciences. His lab now studies the genes of C. elegans and their expression in individual cells. He is a member of the National Academies of Science and Medicine and shared the Gairdner Award with Sulston and others.

Magdalena Zernicka-Goetz, Ph.D. | University of Cambridge

"Building the mammalian embryo - one step at a time"

Abstract: We wish to understand the processes that integrate the development of populations of different cell types into an organism.  Prior to its implantation into the uterus, the mammalian embryo comprises three cell types that begin to be sculpted into an embryo with identifiable parts during implantation, a mysterious process because it is hidden from view. We have recently succeeded in overcoming this limitation by developing an efficient in vitro culture system that allows imaging development from pre- to post-implantation stages outside the body of the mother. In this way we can follow the first morphogenetic steps taken by the pluripotent cell lineages and neighboring extra-embryonic lineages and we have learnt how to mimic several of these using ES cells.  Using this system, we wish to understand the developmental dynamics of individual and groups of cells and the signals that define the positional identity of cells as the embryo continues to develop.

Bio: Magdalena is Professor of Mammalian Development and Stem Cells at the University of Cambridge, UK and Bren Professor of Biology and Biological Engineering at Caltech, California. Her work led to re-define our ways of thinking about the earliest events that govern cell fate specification in the mammalian embryo. She has developed new approaches to culture mammalian embryos in vitro to the point of gastrulation that she has applied to study both mouse and human embryogenesis. Most recently, she has established conditions to allow stem cells representing the three tissues of the embryo to self-assemble and generate 3D embryo-like structures that recapitulate development to gastrulation.