Ido Amit
Krill Prize 2015
Weizmann Institute
Ido Amit
Research Topic:
The coding of immunity in the genome
The coding of immunity in the genome
Executive Summary: Research in my lab aims at understanding how mammals encode complex regulatory functions in their genomes with focus on haematopoiesis and immune responses. For this we combine development of novel single cell methods and models for gene regulation and epigenetic research coupled to computational techniques, modern high throughput sequencing technologies and targeted experiments. Our goal is to uncover fundamental principles of genome function and regulation and how they impact blood development and immune homeostasis in both health and disease. During the first three and a half years at the Weizmann we had been working in several interconnected fields, generally aiming at: (i) understanding mechanisms of transcriptional and chromatin regulation in haematopoiesis and immune response (Nature Biotechnology 2011, Molecular Cell 2012, Nature Biotechnology 2013, Science 2014a, Science 2014b, Molecular Cell 2014 (In Press) Cell 2014 (In Press) and (ii) understanding gene circuits and the cellular complexity controlling immune response (Cell 2011, Molecular Systems Biology 2014, Science 2014c , EMBO 2014 In Press). Additional efforts were devoted to develop novel next generation sequencing approaches for in vivo analysis of chromatin and single cell gene expression dynamics (Nature Communications 2013, Nature Protocols 2013, Science 2014a, Science 2014b and work in progress).
The central hypothesis of our research is that a large number of transcription and chromatin factors form a coordinated genetic network with hematopoietic cis regulatory elements that directs appropriate differentiation and response of hematopoietic cells upon specific environmental cues (Lara et al Science 2014; Lavin et al Cell 2014 In Press). We propose to systematically decipher the underlying molecular principles of chromatin and gene expression dynamics upon both differentiation cues and immune stimuli. These studies will provide the scientific grounds for a better understanding of the molecular basis of haematological and immune pathology (from allergies and viral plagues, to neuronal disorders and diabetes) that are taking an increasing burden on the society. We are studying a set of several ex vivo and in vivo model systems and how they respond to relevant physiological ligands (including both the innate and adaptive system, such as: macrophages, dendritic cells, natural killer cells, B, T cells and many more), this enables us to gain deep insights on diverse regulatory mechanisms employed during hematopoietic and immune decisions. The advanced tools we developed for in vivo transcriptome and epigenetic analysis (Fig. 1) place us in a unique position to measure in vivo RNA and chromatin dynamics during haematopoiesis and immune response. Using modeling approaches, we generate provisional regulatory circuits of proteins and cis regulatory elements controlling these responses, and use genetic mouse models using CRISPR (of both proteins and cis elements) to perform downstream experiments and examine hypotheses derived from our analyses. A central concept, which emerges from many of our recent studies, is the complexity of mammalian chromatin and gene response. This includes cell type specific epiegntic modification of various regulatory elements, multiple feedback mechanisms involving different transcription factors (TF), chromatin factors (CF) and RNA species such as large none-coding RNA, antisense RNA and many more.
The central hypothesis of our research is that a large number of transcription and chromatin factors form a coordinated genetic network with hematopoietic cis regulatory elements that directs appropriate differentiation and response of hematopoietic cells upon specific environmental cues (Lara et al Science 2014; Lavin et al Cell 2014 In Press). We propose to systematically decipher the underlying molecular principles of chromatin and gene expression dynamics upon both differentiation cues and immune stimuli. These studies will provide the scientific grounds for a better understanding of the molecular basis of haematological and immune pathology (from allergies and viral plagues, to neuronal disorders and diabetes) that are taking an increasing burden on the society. We are studying a set of several ex vivo and in vivo model systems and how they respond to relevant physiological ligands (including both the innate and adaptive system, such as: macrophages, dendritic cells, natural killer cells, B, T cells and many more), this enables us to gain deep insights on diverse regulatory mechanisms employed during hematopoietic and immune decisions. The advanced tools we developed for in vivo transcriptome and epigenetic analysis (Fig. 1) place us in a unique position to measure in vivo RNA and chromatin dynamics during haematopoiesis and immune response. Using modeling approaches, we generate provisional regulatory circuits of proteins and cis regulatory elements controlling these responses, and use genetic mouse models using CRISPR (of both proteins and cis elements) to perform downstream experiments and examine hypotheses derived from our analyses. A central concept, which emerges from many of our recent studies, is the complexity of mammalian chromatin and gene response. This includes cell type specific epiegntic modification of various regulatory elements, multiple feedback mechanisms involving different transcription factors (TF), chromatin factors (CF) and RNA species such as large none-coding RNA, antisense RNA and many more.
The overall theme of my lab is to employ novel systematic approaches (Fig.1) to decipher the multiple layers of gene expression and chromatin regulation and their integration in a wide range of in vivo hematopoietic and immune models. Our premise is that such studies will bridge the gap between basic regulatory mechanisms and their in vivo physiological consequences in haematopoiesis and immunology. Using novel single cell RNA-seq techniques we develop, we are constantly pushing the definitions of immune cell types and how they respond to immune challenges (Jaitin et al Science 2014), their developmental origins and mechanism of regulations (work in progress). I have assembled an curiosity driven team of multidisciplinary scientists that study multiple hematopoietic and immune processes at different levels, from holistic view of an ensemble of immune cells responding in vivo to pathogen challenge, to detailed molecular events leading to chromatin and gene activity in specific immune gene locus. Several major questions include: (I) How do TF and CF networks control hematopoietic cell identities? Can we find universal organization principles in such networks? Which parts of the network are more important for tuning cell identities (e.g. the difference between B cell and DC), which are more important for fine-tuning difference between T helper 1 versus T helper 2? Would it be possible to generate a predictive model to understand blood function from DNA sequence? Would such a model explain the impact of mutations/changes in the cis binding landscape (blood regulatory code)? (II) How do immune cells respond to stimuli? How do TF networks in different cell types generate different responses to similar stimuli? Can we find rules in such networks to improve development of adjuvants? (III) The role of regulatory elements in mouse and human and how they feedback to control transcription and chromatin regulation in haematopoiesis and immune response (IV) Identification of novel hematopoietic cell types and unbiased (marker-free) integration of local niche immune responses in physiological and pathological models using single cell RNA-seq. (V) To decipher the complex network of cis and trans elements underlying proper hematopoietic and immune function and how they are perturbed in disease models
