Periodic Reporting for period 4 - HemTree2.0 (Single cell genomic analysis and perturbations of hematopoietic progenitors: Towards a refined model of hematopoiesis)
Reporting period: 2022-04-01 to 2022-09-30
Our work is focused on gaining in-depth and mechanistic understanding of hematopoiesis and immunity at single-cell resolution. Previous and ongoing research in my lab involves developing novel single-cell genomics tools that help us mapping the signaling and transcriptional networks and molecular cues that regulate and control hematopoiesis. This provided us with a reference network model for blood progenitors and their differentiation trajectories during normal and perturbed hematopoiesis, for a better understanding of how heterogeneous groups of immune cells communicate in highly complex systems. As these networks are also defined by their physiological context, we have recently developed novel single cell genomic tools that contribute physical parameters of cellular crosstalk, responses to environmental cues, and tissue location. Single cell studies offer the means to (1) characterize diversity and dynamics within these systems, (2) identify mechanisms of development and regulation, and (3) support careful testing of various immune related mechanisms in both health and disease. Our data and technologies are starting to enable a holistic view of the cell states and regulatory circuits that shape blood differentiation and immune response with which to model these complex cell populations, the crosstalk between them and their impact in human physiology. In line with this vision, we recently: I) identified mechanisms of linage decisions and the involvement of pioneer TF in these circuits; II) uncovered immune cell functions involved in their physiological context; III) measured immune niche dynamics in mouse and human physiology following pathogen stimuli; IV) identified key regulatory elements involved in immune checkpoint that regulate physiological imbalances that lead to autoimmune disease, cancer, and neurodegeneration. Our current work is reshaping the way we understand immunity in health and disease, and we envision that our future work will continue to apply these concepts, models and tools to significantly deepen our understanding in human hematopoiesis and immune function in both health and diseases.
Our research during the lifetime of the proposal was focused on developing new genomic and analytical technologies for precise mapping of the regulatory gene networks that control blood cell development and immune function using in vitro experiments, mouse models and clinical human samples. To this end, we continued to develop novel single cell methods and combine them with computational models, high-throughput sequencing, genome engineering and advanced imaging technologies to uncover fundamental principles of genome function and regulation and to decipher how they impact immune cell development, immune physiology and most importantly how these regulatory mechanisms are perturbed in disease. Using unique technological innovations (described below) allowed us to gain a deeper mechanistic understanding of the immune niches and how cells interact in vivo to provide functional immunity, resolving their complex cellular heterogeneity to find unexpected cellular compositions and states in complex tissues
Our research during the lifetime of the proposal was focused on developing new genomic and analytical technologies for precise mapping of the regulatory gene networks that control blood cell development and immune function using in vitro experiments, mouse models and clinical human samples. To this end, we continued to develop novel single cell methods and combine them with computational models, high-throughput sequencing, genome engineering and advanced imaging technologies to uncover fundamental principles of genome function and regulation and to decipher how they impact immune cell development, immune physiology and most importantly how these regulatory mechanisms are perturbed in disease. Using unique technological innovations (described below) allowed us to gain a deeper mechanistic understanding of the immune niches and how cells interact in vivo to provide functional immunity, resolving their complex cellular heterogeneity to find unexpected cellular compositions and states in complex tissues
Our work from the beginning of the project to the end made important discoveries and publications: I) identified mechanisms of linage decisions and the involvement of these circuits (Giladi A et al Nature Cell Biology 2018); II) uncovered immune cell functions involved in their physiological context (see publications); III) measured immune niche dynamics in mouse and human physiology following pathogen stimuli (Blecher et al., Cell systems 2019) ; IV) identified key regulatory elements involved in immune checkpoint that regulate physiological imbalances that lead to autoimmune disease, cancer, and neurodegeneration (see publications). Our current work is reshaping the way we understand immunity in health and disease, and we envision that our future work will continue to apply these concepts, models and tools to significantly deepen our understanding in human hematopoiesis and immune function in both health and diseases.
Our main objectives included multiple technological development of novel single cell genomic tools to uncover novel pathways and mechanisms of immune dysfunction in cancer. Specifically, we developed next generation genomic profiling coupled with signaling (INS-seq; Katzenelenbogen et al., Cell 2020) and cell-cell interactions (PIC-seq; Giladi et al Nature Biotechnology 2020; Nature Cancer 2021) and spatial transcriptomic analysis (Lopez et al., Nature Biotechnology 2022).
Our main objectives included multiple technological development of novel single cell genomic tools to uncover novel pathways and mechanisms of immune dysfunction in cancer. Specifically, we developed next generation genomic profiling coupled with signaling (INS-seq; Katzenelenbogen et al., Cell 2020) and cell-cell interactions (PIC-seq; Giladi et al Nature Biotechnology 2020; Nature Cancer 2021) and spatial transcriptomic analysis (Lopez et al., Nature Biotechnology 2022).
The immunology field, from very early on, invested great efforts and ingenuity to characterize the immune cell types and elucidate their function, pathways and crosstalk. These discoveries were instrumental for both basic science and immunotherapy. However, resent scientific discoveries from my lab and others indicated that current schemes only partly describe the diversity of immune cell types and their role in physiology and disease, ranging from cancer to neurodegeneration (Jaitin et al., Science 2014; Paul et al., Cell 2015; Matcovitch et al., Science 2016; Gury et al., Cell 2016, Jaitin et al Cell 2016; Medagalia et al., Science 2017; Keren-Shaul et al., Cell 2017; Goldberg et al., Nature Cell Biology 2018; Bornstein et al., Nature 2018; Cohen et al., Cell 2018; Ledergor et al., Nature Medicine 2018; Li et al., Cell 2019). We were the first to develop and apply single cell genomics towards elucidating the diversity of the immune system and demonstrated how single cell technologies can dramatically advance the way we characterize complex immune assemblies and study their spatial organization, clonal distribution, dynamics, pathways, crosstalk and function, in both physiological and pathological contexts (Jaitin et al., Science 2014; Paul et al., Cell 2015; Giladi et al., Cell 2017). For that, we will continue to push the boundaries of single-cell genomic technologies and their implementation in Immunology research; we developed state of the art single cell approaches that combine transcriptional profiles with other modalities such as genome engineering, spatial tissue location, signalling, cell-to-cell interactions and the epigenome. (Medagalia et al., Science 2017 Giladi et al Nature Biotechnology 2020), these are expected to dramatically impact basic immunology and immunotherapy research.