Enabling cell-based therapies through environmental sensing and signal processing

Donahue, Patrick Sean

doi:https://doi.org/10.21985/n2-svmw-b003

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Enabling cell-based therapies through environmental sensing and signal processing

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Cell-based therapies are an exciting frontier in medicine. This field is built on a simple premise—cells can be engineered to recognize and treat various human diseases. The paradigm of cell-based therapy uses biosensors to interrogate a cell’s environment and distinguish disease from health, intracellular signaling pathways and genetic circuitry to process, integrate, and interpret this information, and effector functions to enact a therapeutic response against the disease. Best exemplified at present by chimeric antigen receptor modified T cells, which are programmed to patrol the body and to seek out and destroy tumor cells, cellular therapeutics hold promise for treating cancer and many other pathologies. Though several cell-based therapies have gained FDA approval in recent years for clinical use against hematologic malignancies, the reach of cell-based therapies is limited by many factors, including the availability of fundamental technologies that could enable us to target the cells against a broad range of diseases. This thesis aims to address this problem through two overarching efforts: (I) developing fundamental technologies for cell-based biosensors and therapeutics and (II) translating these cell-based devices for clinical applications. Towards the first aim, I first refined technologies for sensing hallmarks of the tumor microenvironment and discovered that employing different transmembrane domains in a synthetic receptor system could mitigate ligand-independent signaling. This advance will enhance the specificity, and thereby safety, of cell-based therapies that rely on synthetic, transmembrane receptors to sense their environments. I also investigated biosensors for detecting hypoxia, a feature common to many cancers and other pathologies, elucidated several principles for engineering these sensors, and designed genetic circuits to modulate their signaling. These circuits may ultimately make these biosensors more robust and resultingly expand the range of applications for this technology to many disease indications. Finally, I developed a toolkit for the engineering of genetic programs in mammalian cells. Through a thorough investigation and characterization of synthetic promoters and transcription factors, I established principles for tuning this system and enabled the design of a mathematical model that predicts how these components and circuits function. This toolkit, termed the Composable Mammalian Elements of Transcription (COMET), has broad applications for composing genetic circuits that form the signaling pathways in cell-based therapies, including those that convert the signaling from biosensors into an effector function. Towards the second aim, I developed a natural killer cell-based strategy that can be deployed against a broad range of solid tumors. Microenvironment induced natural killer cells (MINK) recognize hallmarks of the tumor microenvironment (TME), such as hypoxia, rather than tumor cell-surface antigens, and respond with a therapeutic effector function, such as producing a cytokine to stimulate an immune response against the tumor. By relying on features that arise from tumor physiology and are thus common across tumors rather than on tumor-specific antigens, MINK and other tumor TME-recognizing therapies may find wide utility. As evidenced by MINK, the technologies developed in this thesis enable the engineering of cell-based therapies against cancer; these synthetic biology technologies will ultimately enable the development of cell-based therapies against a broad range of diseases.

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