Programming gene and engineered-cell therapies with synthetic biology

BACKGROUND Gene and engineered-cell therapies promise new treatment modalities for incurable or difficult-to-treat diseases. First-generation gene and engineered-cell therapies are already used in the clinic, including an ex vivo gene-replacement therapy for adenosine deaminase deficiency, chimeric antigen receptor (CAR) T cell therapies for certain types of leukemias and lymphomas, an adeno-associated virus gene therapy for inherited retinal diseases, and investigational therapies for β-thalassemia, sickle cell disease, hemophilia, and spinal muscular atrophy. Despite these early successes, safety concerns may hamper the broader adoption of some of these approaches: For example, overexpression of a therapeutic gene product with a narrow therapeutic window may be toxic, and excessive activation of T cells can be fatal. More-sophisticated control over cellular activity would allow us to reliably “program” cells with therapeutic behaviors, leading to safer and more effective gene and engineered-cell therapies as well as new treatments. ADVANCES Recent advances in synthetic biology are enabling new gene and engineered-cell therapies. These developments include engineered biological sensors that can detect disease biomarkers such as microRNAs and cell-surface proteins; genetic sensors that respond to exogenous small molecules; and new methods for interacting with various components of the cell—editing DNA, modulating RNA, and interfacing with endogenous signaling networks. These new biological modules have therapeutic potential on their own and can also serve as building blocks for sophisticated synthetic gene “circuits” that precisely control the strength, timing, and location of therapeutic function. This advanced control over cellular behavior will facilitate the development of treatments that address the underlying molecular causes of disease as well as provide viable therapeutic strategies in situations where the biomolecular targets have been previously considered “undruggable.” Recent publications have demonstrated several strategies for designing complex therapeutic genetic programs by combining basic sensor, regulatory, and effector modules. These strategies include (i) external small-molecule regulation to control therapeutic activity postdelivery, (ii) sensors of cell-specific biomarkers that activate therapeutic activity only in diseased cells and tissues, and/or (iii) feedback control loops that maintain homeostasis of bodily systems. Example therapeutic systems include a genetic circuit that senses two specific cell-surface markers to activate CAR T cells only in the presence of target cancer cells, a circuit that programmatically differentiates pancreatic progenitor cells into insulin-secreting β-like cells, and a gene network that senses the amount of psoriasis-associated cytokines to release immune-modulatory proteins only during flare-ups. These proof-of-concept systems may lead to new treatments that are dramatically safer and more effective than current therapies. OUTLOOK Rapid progress in synthetic biology and related fields is bringing therapeutic gene circuits ever closer to the clinic. Ongoing efforts in modeling and simulating mammalian genetic circuits will reduce the number of circuit variants that need to be tested to achieve the desired behavior. The platforms used to test genetic circuits are also evolving to more closely resemble the actual human environment in which the circuits will operate. Human organoid, tissue-on-a-chip, and whole-blood models will enable higher-throughput circuit characterization and optimization in a more physiologically relevant setting. Progress in nucleic acid delivery will improve the safety and efficiency with which therapeutic nucleic acids are introduced to target cells, and new methods for immunomodulation will suppress or mitigate unwanted immune responses. Together, these advances will accelerate the development and adoption of synthetic biology-based gene and engineered-cell therapies.