Thursday, September 5, 2013

Synthetic Biology's "Pre-Industrial" Age

Because synthetic biologists are largely preoccupied with understanding how to make synthetic network connections, one issue that has been largely overlooked is that of how a synthetic circuit, once introduced into a host, interacts with the native cellular environment—what we like to call the circuit’s context. A critical question for synthetic biology will be: How do we engineer for context?
The Scientist:
Historically, a focus of synthetic biology has been the construction of molecular logic circuits in bacteria, including switches, oscillators, logic gates, filters, analog circuits, and many other electronics-mimicking genetic devices. Researchers are now attempting to integrate these small computational circuits to enable more sophisticated information processing and computational power within cells. An exciting new focus is using synthetic approaches to understand the organizational principles of eukaryotic cells and higher-order cellular systems. For example, researchers at the University of California, San Francisco, recently used a synthetic biology approach to interrogate the phenomenon of cell polarization, or the ability of cells to asymmetrically organize their components. From a toolkit of engineered signaling proteins known to be involved in this process, the team constructed synthetic circuits and looked for the circuit motifs that were capable of producing strong, sustained cell poles in yeast.

Other synthetic biologists have assembled similar metabolic pathways in cells in hopes of turning microbes into living factories for the production of biofuels and other chemical goods. Another field that now seems poised to undergo a revolution by the forward engineering of cells is biomedicine. Cells naturally perform therapeutic tasks in the body—immune cells identify and remove pathogens, for example—and unlike drugs or molecules, cells can perform complex functions, such as sensing their environments or proliferating. Indeed, patient-specific immune cells are already being genetically engineered with receptors called chimeric antigen receptors (CARs) that allow them to target and destroy tumors in the body. Synthetic circuits and approaches could be used to further enhance these cancer-fighting functions and/or make these cell-based therapies safer.

Synthetic biology could also be used in cancer diagnostics. For example, researchers recently engineered into human cells gene circuits that are triggered by microRNA signatures unique to certain cancers. Similar approaches could be envisioned for endowing cells with sense-and-response capabilities to detect and mediate a number of other dysfunctions and pathologies. Promising opportunities for cell-based therapeutics also include patient-specific stem cells for regenerative medicine and microbiome engineering to treat gastrointestinal diseases.

What’s more, all of these exciting efforts are occurring simultaneously with our now unprecedented ability to make modifications to the genomes of cells. Using targeting tools, such as zinc fingers, TALEs, and CRISPR/Cas, researchers can now edit specific genes within a genome with very high precision. For example, we can—and do, in the form of gene therapy—use these tools to inactivate genes known to be involved in disease progression or in pathogen life cycles. We can also use them to introduce synthetic circuits into precise locations within a variety of genomes, including in human cells—a feat that would have been impossible less than a decade ago. We can even think about de novo designing and sculpting of genomes to have desirable properties.

But we have a long way to go. While engineers of mechanical and electrical systems have common engineering principles (standardization of building components, simplicity and modularity in design, reliability) to guide their designs, no such unifying principles or design frameworks exist for the engineering of biological systems. Although some parts such as zinc fingers have easy-to-engineer, modular designs, many others do not. Furthermore, because a complete systems-level understanding of biology is unavailable, anticipation of interactions between a synthetic circuit and the intracellular environment is impossible.

Ultimately, in considering how to engineer functions in living cells, the only truly unifying design rules may be those gleaned from the blueprints provided by nature. There is evidence that evolution has shaped the design of natural systems through iterative “tuning,” whereby biological parts have been introduced, modified, and assembled over and over again to arrive at systems that are optimized for both function and context. These natural solutions, such as zinc fingers, may be the best starting points for engineering synthetic systems. Similarly, by experimentally tinkering with the existing natural blueprints, we, as synthetic biologists, can find out what works in an engineered context.

In this “preindustrial” era of synthetic biology, it’s hard to know the limitations of engineered biological systems. Yet, it’s important to note that a full physical understanding of how biological parts interact and operate may not be necessary for realizing synthetic biology as an established engineering discipline. In fact, metallurgy became an established craft, allowing us to reliably fashion metals, long before an atomistic picture of the materials was uncovered. Similarly, our understanding and practice of biology has matured to an exciting point: we are poised to establish reliable design rules for building on nature.

Ahmad S. Khalil is an assistant professor in the Department of Biomedical Engineering and the deputy director of the Center of Synthetic Biology at Boston University. Caleb J. Bashor is an HHMI postdoctoral associate in the Department of Biomedical Engineering and Center of Synthetic Biology at Boston University. Timothy K. Lu is an assistant professor in the departments of Electrical Engineering & Computer Science and Biological Engineering at the Massachusetts Institute of Technology.

More information:
» George M. Church: "Evolving Engineering"
» J. Craig Venter: "Synthesizing Life"

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