In Vivo Gene Editing and Immunotherapy
Department of Genetics, Systems Biology Institute, & Cancer Center, School of Medicine
In Vivo Gene Editing and Immunotherapy
T cells became the central focus of new cancer therapeutics. Immune checkpoint inhibitors targeting T cell signaling pathways and cellular therapeutics utilizing chimeric antigen receptors (CARs) have shown success in the clinic. Discovery of previously unknown genes that modulate T cell function is of urgent need to open different avenues for immunotherapies, as a large fraction of patients still do not respond to, or have undesired side effects to currently approved ones. Systematic approaches to identify new regulators of T cell functions in vivo can provide potentially orthogonal or complementary opportunities. We recently performed in vivo CRISPR screens in CD8 cytotoxic T cells, both in a genome-scale and in a focused manner, in tumor models of immunotherapy (Dong et al. 2019 Cell). Furthermore, we developed a novel AAV-SleepingBeauty system that enhanced the power of genetic screening in primary T cells (Ye et al. 2019 Nature Biotechnology). Our screen re-discovered prime immunotherapy targets such as PD-1, TIM-3 and LAG3, as well as previously undocumented targets. We characterized novel targets such as DHX37, ODC1, MGAT5 and PDIA3 for their activity in mouse and human CD8 T cells including CAR-Ts.
Current major types of immunotherapy include checkpoint blockade, adoptive cell transfer, human recombinant cytokines, and cancer vaccines. However, immunotherapy has met challenges in immunologically cold tumors. These challenges urge for new types of immunotherapies that are more potent and potentially less toxic. Recently, we have developed CRISPRa-mediated Multiplexed Activation of Endogenous Genes as an Immunotherapy (MAEGI) (Wang et al. 2019 Nature Immunology, in press). The CRISPR activation (CRISPRa) system uses a catalytically inactive Cas9 (dCas9), enabling simple and flexible gene expression regulation through dCas9-transcriptional activators paired with single guide RNAs (sgRNAs). This enables precise targeting of large gene pools of endogenous genes in a flexible manner. We demonstrate that MAEGI has therapeutic efficacy across three tumor types. Mechanistically, our preliminary work showed that MAEGI treatment elicits anti-tumor immune responses by recruiting effector T cells and remodeling the tumor microenvironment. We will perform advanced development, characterization and optimization of MAEGI, as a novel immune-gene therapy approach to elicit a potent and specific immune response to tumors based on their unique genetic composition.
Sidi Chen joined the Yale Faculty in 2015 as an assistant professor in the Department of Genetics and Systems Biology Institute, also as a member of the Yale Cancer Center and the Yale Stem Cell Center. Chen earned a PhD in evolutionary genetics from The University of Chicago with an award-winning dissertation with Dr. Manyuan Long. After graduation he performed postdoctoral studies at MIT under the mentorship of Dr. Phil Sharp, and also the Broad Institute working with Dr. Feng Zhang. His research focuses on providing a global understanding of biological systems. Chen developed and applied genome editing and high-throughput screening technologies, precision CRISPR-based in vivo models of cancer, global mapping of functional drivers of cancer oncogenesis and metastasis. More recently, he developed novel systems that enable rapid identification of novel immunotherapy targets and new modalities of cancer immunotherapy. Dr. Chen received a number of national and international awards including the NIH Director’s New Innovator Award, DoD Era of Hope Scholar Award, Damon Runyon Cancer Research Fellow, Dale Frey Award for Breakthrough Scientists, AACR NextGen Award for Transformative Cancer Research, TMKF Innovative/Translation Cancer Research Award, BCA Exceptional Research Grant Award, MRA Young Investigator Award, V Scholar, Bohmfalk Scholar, Ludwig Family Foundation Award, St. Baldrick’s Foundation Award, CRI Clinic & Laboratory Integration Program (CLIP), MIT TechReview Regional 35 Innovators, Yale-Blavatnik Innovator Award, and Sontag Foundation Distinguished Scientist Award.