Mapping cellular communication at single-cell resolution through novel CRISPR systems

项目总结/文摘

Project Summary/Abstract Mapping cellular communication at single-cell resolution through novel CRISPR systems The Fellmann lab focuses on decoding principles of cellular signaling in disease progression and therapy, and pioneering of CRISPR-Cas and RNA interference (RNAi) systems. For over a decade, my research has centered on better understanding RNA-guided immune systems and establishing innovative strategies to dissect disease, many of which have found broad application among the scientific community. My lab currently studies the interplay between Cas enzymes and DNA repair pathways to develop novel approaches for genome editing and precision medicine. We apply these quantitative, high-throughput methods to study the plasticity of signaling networks in health and disease, with the goal of translating insights into breakthrough therapies for patients. A persisting challenge in biology is recording molecular information in a cell-specific manner without disrupting the system under study. To overcome this, we propose transformative CRISPR platforms to track host-pathogen interactions and map pathway deregulation in human disease. The approaches rest on the development of Cas9 and guide RNA systems that are responsive to 1) pathogen-specific proteases (“ProCas9s”) or 2) mammalian cell-signaling events (“CRISPR-capture”), thereby enabling the recording of a cell’s history by inscribing marks at predetermined loci in the genome. As rapid response to emerging viral threats, we will develop a ProCas9 that can autonomously record SARS-CoV-2 infections and label respective cells. We will use this strategy to dissect long-term consequences of viral infection in cardiomyocytes. To enable general mapping of cellular communication, we propose a novel data recording methodology termed CRISPR-capture that places the expression of sgRNAs under the control of RNA polymerase II promoters, rather than the conventionally used RNA Pol-III promoters. Since mammalian signaling outputs are largely based on transcription factors regulating Pol-II promoters, CRISPR-capture tunes Cas activity to a cell’s state, providing the unique ability to map cellular signaling at single-cell resolution and monitor key biological events over the lifetime of a cell for the first time. Ultimately, we will leverage CRISPR-capture to monitor individual cells in four dimensions (space-time) during disease progression and treatment, to uncover organizational principles of tissue heterogeneity and establish new therapeutic strategies for patients. My multidisciplinary training in genome editing with Dr. Jennifer Doudna (University of California, Berkeley), functional genomics with Dr. Scott Lowe (Cold Spring Harbor Laboratory), and in-vivo animal models of human disease, allows me to bridge fundamental biology and patient-centered research. Moreover, my experience as co-founder and Chief Scientific Officer of a successful start-up company taught me invaluable lessons that will serve me well in directing and completing the proposed studies. Importantly, I am deeply committed to mentoring and serving as a role model for a talented and diverse group of next-generation scientists, and to providing equal opportunities to all.