Engineering Therapeutic Human Immune Cells with Modular Self-contained Genetic Circuits

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PROJECT SUMMARY/ABSTRACT Current strategies to engineer human cell-based therapeutics rely upon the delivery and subsequent genomic integration of transgenic payloads. Although these approaches have catalyzed transformative medical advances, the integration of transgenic DNA permanently disrupts natural genomic sequences and can lead to unexpected and even hazardous consequences. In addition, integrated transgenic DNA is often unpredictably expressed and is prone to epigenetic silencing over time, especially within primary human immune cells. Furthermore, existing approaches to validate large transgenic genomically- integrated DNA cargoes are inefficient and costly. These critical barriers limit the extent to which human cells can be repurposed and engineered as cell-based therapeutics and these challenges are preventing biotechnological and clinical innovations. Non-integrating, double-stranded DNA viruses have evolved sophisticated solutions to these critical barriers, and they can stably persist within human cells as circularized self-contained episomes across cellular divisions and for the lifetime of infected hosts. These viruses accomplish this remarkable persistence by tailoring their own gene expression patterns, synchronizing their genomic replication, and by reshaping the endogenous transcriptional networks of host cells. In this proposal, we will harness these natural abilities and refine them using clinical-grade gene therapy vector testbeds. Our approach will establish an entirely new way to use of circular, orthogonal episomal DNA within human cells. In Aim 1 of this proposal, we design, build, test, and optimize genetically-encoded episomal modules to enable i) site-specific and tunable genomic localization, ii) programmable episomal replication, and iii) multi-layered safety switches, within clinically validated integrase-deficient lentiviral (IDLV) and high- capacity adenoviral (HcAdV) gene therapy vector testbeds. In Aim 2 of this proposal, we will build genetic circuits within IDLV and HcAdV gene therapy vectors that sense hypoxic environments and/or small molecules and respond to these signals in real time by producing fluorometric diagnostics and/or synthetic CRISPR/Cas9-based transcription factors to drive the expression of therapeutically crucial cytokines or biomedically relevant phenotypic changes. In each independent Aim, we will use experimental techniques at the interface of functional genomics, genome engineering, and synthetic biology. To preserve and maximize the therapeutic utility of our results and to ensure applicability beyond the scope of this proposal, both Aims will be carried out using primary human T cells and mesenchymal stromal cells. Collectively, this project will combine engineering principles and lessons from biomedical sciences to spur advances that will be broadly useful to biomedical researchers, actionable for clinicians, and meaningful to future patients in need of sophisticated cell-based therapeutics.