Why I believe in cell-free biology
Cell-free biology is redefining what is possible in the discovery of tomorrow’s therapeutics and chemicals.
I have always been fascinated by our ability to engineer our surroundings, how we can convert something as simple as rocks into concrete and skyscrapers. Or how a mineral, silicon, has powered the explosion of the digital economy.
Scientists made these applications possible by engineering microbes, living organisms. Living organisms are to biology as silicon has been for computers, the fundamental unit of engineering. Cells come with many attractive features — the ability to grow and divide, the ability to evolve. But the problem with living organisms is that they would rather do what 3.5 billion years of evolution have taught them to do, which is often not what we want them to do. This makes engineering them very time-consuming.
Cell-free biology is fascinating to me as a fundamental and foundational alternate to engineering microbes. As the name implies, cell-free biology is the engineering of biology without the cell. Surprisingly, biology does not need living organisms to work. Rather, the components of the organism, the basic building blocks of life — proteins, DNA, water, and food — can all be mixed together to do many of the activities we associate with biology. What is a complicated biological problem can be simplified into a simpler chemical problem. Practically, unlocking the potential of engineering molecules becomes way easier.
Currently, cell-free biology is commercially used to make existing chemicals and therapeutics more effectively and efficiently. Because cell-free systems cannot reproduce, one can make stuff that would otherwise be toxic to living cells. Two companies, Sutro Biopharma (NASDAQ: STRO) and Greenlight Biosciences have proven this point at commercial scale. Sutro has managed to produce oncology-related antibodies in fermenters of cell-free systems, at the scales that one brews beer. On the other hand, Greenlight Biosciences is pioneering the production of RNA for pest control.
However, cell-free biology does not only make it easier to make existing chemicals and therapeutics, but also entirely new ones. Commercially, companies like Synthorx (NASDAQ: THOR) and PeptiDream utilize cell-free systems to produce therapeutics that do not yet exist in nature. They do this by taking advantage of a cell-free platform’s ability to substitute naturally occurring amino acids, foundational units for proteins, for non-naturally occurring ones engineered to have therapeutic properties. This is exciting, as these therapeutics cannot be produced using other technologies.
As cell-free systems hit cost benchmarks — as they produce cheaper chemicals — one can envision future opportunities for the technology. Research is already underway to use cell-free systems to make solvents and polymers. Future aspirational goals include using cell-free biology to replace the need entirely for using animals as food, or for cell-free biology to power carbon capture.
Cell-free biology is not a new idea. In fact, it outdates cellular biology as a tool, and was the original way we understood our biological surroundings. Two Nobel Prizes were won using it: in 1968, for discovering the amino acid code, and in 2006, for describing eukaryotic transcription. But it is new surrounding technologies — to print DNA, to sequence DNA, to automate laborious tasks, to learn from massive computing power — that make this technology worth revisiting today as a foundational research tool.
Even with all of the sequencing data we have collected (and the resulting genomics, proteomics, and other -omics fields that have spawned), our understanding of biology is still extremely limited. Cell-free biology allows the simplification of complex systems into discrete units where hypotheses can be tested. The level of simplicity is tunable by the user. For basic hypotheses, a minimal, defined cell-free system can be used, while for bigger system-level hypotheses, more complex and undefined cell-free systems can be made. Critically, cell-free systems are consistent — unlike cells, every cell-free system produced in the same manner behaves the same.
The simplicity of cell-free biology allows it to be a powerful data generation tool. Not needing to wait for cellular growth means experiments can be done in hours rather than days. In addition, not needing to fight a cell’s innate desire to grow, divide, and evolve means 1000 experiments can be done in cell-free systems with the same effort it takes for one experiment in cells. This means more data to understand biological complexity.
Three elegant applications arise from using cell-free biology to understand our world. First, scientists are working to understand how life started by using cell-free biology to prototype the first cell, or “protocell.” Starting at the minimum set of items needed, can one understand life by resurrecting growth and division? Second, cell-free biology is being used to produce genetic circuits; in many ways, analogs to traditional circuits but with applications in controlling engineered cells. This has immediate applications for controlling the activity of microbes, or for engineering T-cells to activate or suppress for cancer treatments. Finally, cell-free biology can be used to help build understanding of biology, by teaching biological fundamentals to high school students. Biology becomes a programmable toy, where different instructions, encoded in DNA, allow students to produce different colored outputs. Only water and a pre-prepared cell-free system are needed to produce results.
Cell-free biology is exceptionally robust. We now know that cell-free systems can be “freeze-dried” into stable, paper strips that can be deployed, room temperature, in the same way a pregnancy test can. Additionally, unlike with cells that can grow and contaminate the environment, cell-free systems are dead and cannot replicate, mitigating concerns about the release of genetically modified organisms.
It is this intriguing feature that has been studied by groups as a way to sense biological threats without the use of expensive equipment. These can detect threats to health like Zika. In the future, one can imagine cell-free systems made in this way playing a critical role in the personal health revolution, where cell-free biology can be used to sense issues in your genomic information by functionalizing the activity of genes in real-time for your doctor. A variation of this already exists, where cell-free biology is being used to manufacture medicines “on-demand.” A freeze-dried cell-free system and an envelope of instructions can allow those in resource limited environments (places without power, or even space) to produce things on the personal-use scale that otherwise would require resource-intensive factories.
As a physician-scientist, the ability of cell-free biology to mine molecules from nature excites me the most, and drives the mission of Tierra Biosciences (formerly Synvitrobio), the company I lead. The most important compounds we use as a society are produced by the plants and microbes that surround us — things from the mundane, like caffeine, to things as important as penicillin to treat disease and pesticides to protect crops. However, we’ve been finding fewer and fewer molecules, leading to crises such as antibiotic resistance. In the US every year, at least 23,000 people die from infections we used to be able to treat.
The diversity on our planet, however, is vast, an estimated 1 trillion unique species, each with the capacity to produce new antibiotics and other molecules. However, we have only scratched the surface of this diversity. As biologists, we routinely work with only 10 species, and the vast majority of the others (99.999999%) we cannot grow. If we can unlock this diversity, can we unlock a new golden era of identifying natural products?
To me, it is exciting that the instructions for making all of the new molecules already exist. They are just encoded in a “treasure-map” that needs to be followed — DNA. Microbes use their own DNA to determine what molecules to make in order to survive in their environments. Given advances in next-generation sequencing, we now know much of this DNA, and almost all of it, including that found on New York City subways, remains uncharacterized. Here is where I think cell-free biology shines, as a tool to rapidly search this DNA for molecules. Utilizing the hyper-throughput property of cell-free biology, at Tierra we’re looking to build a search engine of sorts, that can screen through this DNA and effectively functionalize it to make molecules that nature has evolved but that we have not yet found. We envision a new golden era of natural products, that will bring new antibiotics, therapeutics, and other molecules to market.
With so many avenues of cell-free biology being developed and more future applications yet unknown, it is an exciting time to work in this field. I believe in cell-free biology because it is fundamental to our future. As the field grows, I have been thrilled to see growing numbers of cell-free enthusiasts at conferences and workshops sharing their research. We are starting to see dedicated funding from federal agencies ranging from the Departments of Defense to the Department of Energy to explore its potential. Continued government funding of this area, especially in areas of basic science and health, is critical for cell-free biology to reach its full potential.
With thanks to Mary Catherine O’Connor, Angela Du, and Richard Murray for feedback