Gene Circuits Empower Next-Generation Cell and Gene Therapies

Senti Biosciences describes how “living drugs” may be programmed to fulfill user-defined functions

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Tim Lu
Tim Lu, MD, PhD
Co-founder and CEO
Senti Biosciences

Over the past few decades, we have seen remarkable advances in technologies for reading (sequencing) and writing (synthesizing) DNA. These technologies have enabled us to decipher disease. Now they are allowing us to program “living medicines” —cell and gene therapies that reprogram genetic code.

Traditional drugs, namely, small molecules and biologics, typically target proteins and block their function. These drugs are static. They have a predefined activity that can’t be adapted once they are delivered into patients. Living medicines, however, are dynamic. That is, they provide sense-and-respond functionality.

As transformative as living medicines promise to be, they are still confined to narrow applications, having been of proven effectiveness against only a few monogenic diseases and hematological malignancies. Current approaches are limited to sensing and correcting single disease signatures, and they provide little control over their dosage, timing, or localization. These shortcomings can be overcome if synthetic biology is used to create the next generation of cell and gene therapies. These therapies will be programmable, and when they are broadly adopted, they will help treat, or even cure, many complex diseases.

Programming cell and gene therapies with synthetic biology

Synthetic biology applies engineering principles to program living systems, enabling them to perform user-defined functions. By leveraging advances in our ability to read and write DNA, we can engineer cells that incorporate artificial multigene constructs, referred to as gene circuits, that allow cells to make decisions and produce a desired response.

Gene circuits that carry out sophisticated functions are built up from smaller submodules. For example, a simple sense-and-respond gene circuit can be conceptualized as a system that consists of three distinct modules:

  • A sensing module that detects disease biomarkers.
  • A computational module that transforms inputs into outputs, for example, by implementing Boolean logic, where a specific combination of inputs produces a defined output, or analog computing, where the output corresponds to a continuously variable input, similar to a rheostat.
  • An output module that executes one or more therapeutic functions.
Gene circuits
Gene circuits are multicomponent biological constructs that sense inputs and generate outputs. In this diagram, the inputs are shown on the left, the gene circuits are shown in the center, and the outputs are shown on the right. Notice that a gene circuit’s user-defined functionality may include the secretion of molecules that enable feedback regulation. [Senti Biosciences]

Gene circuits functionally enhance cell and gene therapies

Gene circuits are the “software” that can be deployed into virtually any cell or gene therapy modality (the “hardware”) to create adaptive therapies that can address many different disease areas. Programming biological systems with gene circuits can overcome the shortcomings of existing cell and gene therapy approaches by making them more controllable, targeted, and effective via multimodal activity.

Enhanced controllability: As remarkable as current cell and gene therapies are, they can also lead to severe side effects. The lack of precision in targeting, coupled with the persistence of these living medicines in the body, can result in undesirable outcomes. This problem is exacerbated by the fact that they cannot be easily controlled after administration.

To address this issue, researchers at the University of California, San Francisco, engineered a small molecule responsive on switch into chimeric antigen receptor (CAR) T cells.1 This gene circuit can be used to titrate the activity of the CAR T cells, depending on the amount of small molecule present.

An alternative sense-and-respond approach was demonstrated by Schukur et al.2 They designed a gene circuit that quantifies the levels of two proinflammatory cytokines in psoriatic tissues, integrates these inputs using a synthetic and gate, then triggers the expression of therapeutic levels of anti-inflammatory cytokines only when both inputs are simultaneously present. The cells engineered with this circuit prevented psoriatic flares, improved existing skin lesions, and restored normal skin morphology in mice.

Precision targeting: Complex diseases, such as cancer, are heterogeneous, both at the inter- and intrapatient levels. Two patients diagnosed with the same type of cancer—and even two adjacent sections of an individual patient’s tumor—can be genetically distinct from one another and have different molecular signatures. Additionally, these signatures can be present in healthy tissues.

Because current therapies typically target only a single tumor-associated signature, they are poorly equipped to deal with such heterogeneity, which can result in limited efficacy (due to the inability to completely target the entire tumor) and significant toxicity (due to killing of healthy tissues).

To enhance efficacy and reduce tumor escape, a cell therapy can be equipped with an or logic gene circuit that kills cells that express any one of multiple tumor antigens. To improve specificity, a cell therapy can be engineered with a not logic gene circuit that spares healthy cells by recognizing healthy tissue antigens. This was demonstrated by Cho et al. when they engineered a “SUPRA CAR”—a split, universal, programmable CAR system that can recognize multiple antigens and perform combinatorial logic before triggering T-cell activity against tumors.3

Multiple mechanisms of action: Conventional immunotherapy approaches rely on inhibiting or activating a single pathway to target cancer cells. However, tumors have developed multiple ways of evading the immune system, necessitating an arsenal of different mechanisms to achieve a sustained therapeutic response. Although combination therapy with conventional modalities, such as small molecules and biologics, can target multiple pathways, it poses translational challenges as it requires delivery of multiple individual agents, which may all have distinct pharmacokinetic properties, and a complex clinical development path.

Senti Biosciences recently developed a gene circuit–based allogeneic cell therapy, SENTI-101, for ovarian cancer patients.4 SENTI-101 homes in on tumors and is programmed by a gene circuit to express high levels of two complementary, immunostimulatory cytokines within the tumor at concentrations that are much higher than those found in systemic circulation. This single medicine, which combines the activity of multiple cytokines, elicits a robust antitumor immune response involving multiple mechanisms of action mediated by different immune cell types, resulting in a significant reduction of tumor burden, prolonged survival, and induction of immune memory.

The ability to regulate the activity, timing, and localization of cell and gene therapies is an active area of research that will make these therapies safer, more efficacious, and ultimately dynamically responsive to disease conditions.

Scalable circuit-generating workflow

For intelligent cell and gene therapies to fulfill their transformative potential, it is important to have an efficient workflow for designing and building therapeutic gene circuits, testing them in relevant disease models, and optimizing their design based on the results. Traditionally, this is treated as a linear, sequential process.

Senti Biosciences is tackling this problem with a centralized computational design platform for gene circuits, coupled with parallelized synthetic biology, viral and cell manufacturing, in vitro biology, and in vivo animal modeling. By standardizing design specifications and data collection, this platform enables informatics that can learn from each design-build-test cycle, ultimately accelerating the convergence toward robust therapeutic circuits with optimized efficacy and safety profiles.

The future of cell and gene therapy

Thanks to advances in synthetic biology, creating intelligent, living medicines is no longer a pipe dream. With the democratization of biological programming, one can envision a future where we have a repertoire of gene circuits that can be rapidly optimized for a given indication and can treat patients whose diseases have, until now, been considered intractable.

 

Tim Lu, MD, PhD, is co-founder and CEO of Senti Biosciences.

References
1. Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. Remote control of therapeutic T cells through a small molecule–gated chimeric receptor. Science 2015; 350(6258): aab4077. DOI: 10.1126/science.aab4077.
2. Schukur L, Geering B, Charpin-El Hamri G, Fussenegger M. Implantable synthetic cytokine converter cells with AND-gate logic treat experimental psoriasis. Sci. Transl. Med. 2015; 7(318): 318ra201. DOI: 10.1126/scitranslmed.aac4964.
3. Cho JH, Collins JJ, Wong WW. Universal Chimeric Antigen Receptors for Multiplexed and Logical Control of T Cell Responses. Cell 2018; 173(6): 1426-1438.e11. DOI: 10.1016/j.cell.2018.03.038.
4. Junca AG, Lee G, Nagaraja A, et al. SENTI-101, an allogeneic cell product, induces potent and durable anti-tumor immunity in pre-clinical models of peritoneal carcinomatosis. 34th Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2019): Part 1. J. ImmunoTher. Cancer 7, article no. 282. DOI: 10.1186/s40425-019-0763-1.

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