Research
Research Overview
Multicellularity as fundamental biology
Individual cells require specialized behaviors to achieve a multicellular lifestyle in the face of evolutionary pressure to compete against one another. Conversely, “failures of multicellularity” underlie inherently multicellular diseases like cancer, autoimmunity, and hormonal dysregulation. In these diseases, individual cells grow, kill out of control, or miscommunicate to the detriment of the multicellular organism. How do single cells collectively manage these challenges? What unifying principles might govern behaviors common to biofilms, colonies, and animals? These questions are difficult to answer in natural systems due to complex, overlapping regulation pathways.
My approach to address these fundamental questions is to engineer multicellular behaviors one-by-one into otherwise single-celled, planktonic E. coli. This effectively decouples multicellular mechanisms like cell-cell adhesion, cell-cell signaling, and differentiation. Decoupling enables a high level of control, simplifying the identification of key components in multicellular lifestyles.
Multicellularity as engineering
These same questions can be framed as an engineering challenge. Synthetic biologists have engineered increasingly complex logic circuits and metabolic pathways into individual cells. As engineered circuits have grown in size, host-cell burden has begun to constrain their design. Multicellular organisms solve this constraint by division of labor into multiple cell types. However, engineering multicellular behaviors into a single-cell chassis faces complex hurdles. To maintain circuit stability, cell types must maintain constant ratios, avoid competition for resources, and suppress cheater mutations. These are fundamental issues that multicellular organisms have evolved to overcome, but that synthetic biology has yet to fully address.
I develop tools and systems that demonstrate solutions to these fundamental problems by engineering minimal multicellular-like behaviors into E. coli. This will enable development of complex metabolic consortia, living materials, and artificial tissues, which require precise control and evolutionary stability of multicellular groups.
Spatial structure
What are the most efficient ways to generate spatial structure? How can we engineer structured 2D and 3D communities across scales?
Natural multicellular patterns are often formed by complex interactions of cells that involve a combination of cell-cell adhesion, cell-cell signaling, differentiation, cell growth, cell movement., and force generation. But what ranges of patterns can a single type of interaction produce on its own? Adhesion can produce arbitrary self-assembly (Cell 2018) and population interface (Nature 2022) patterns with very few adhesin pairs. What about differentiation? Can one predict the types of abnormal structures generated by cancerous cheater cells? These are questions that are hard to answer rationally without the aid of mathematical models and controlled experimental systems.
Relevant publications
Cell 2018
Multicellular toolkits
What are the minimal mechanisms necessary for multicellularity? How can we engineer precise control over cell-cell interactions?
Building multicellular tools from the bottom up in single-celled organisms gives the flexibility and control to address fundamental questions. Many tools that cells in multicellular organisms use to interact with each other have not been brought under synthetic control. I developed powerful tools for adhesion (Cell 2018) and evolutionarily stable differentiation (Cell 2024). Other groups have developed tools for diffusible signaling (via quorum sensing) and other (evolutionarily susceptible) types of differentiation. Can we develop systems for juxtacrine signaling in E. coli, the workhorse of synthetic biology? What fundamental biophysical tradeoffs exist between adhesion and juxtacrine signaling, which in multicellular organisms are usually coupled within the same molecules (e.g, cadherins or Delta-Notch)? These questions can be most easily addressed using synthetic, controllable, decoupled tools.
Relevant publications
Cell 2024
A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover.
Fitness landscaping
How do cells cooperate despite evolutionary pressure to compete? How can we engineer production of evolutionarily stable consortia?
Multicellular organisms can contain trillions of cells that cooperate without serious threat from cell-cell competition for decades and even centuries. I demonstrated a cell-autonomous method to prevent non-differentiating stem-cell cheaters over long time periods (Cell 2024). How else can we recreate intercellular cooperation? Many theories of cooperation rely on cells being able to recognize cheating behavior in other cells and respond in various ways. For example, in autoimmune surveillance, immune cells kill other cells of the self if they behave inappropriately. Could we build a bacterial immune-like system to protect industrial cultures from pathogens and cheaters? What are the minimal requirements for doing so? These questions rely on "fitness landscape engineering" — engineering circuits that behave in defined ways when they mutate or are placed in new environments.
Relevant publications
Cell 2024
Unifying regulatory motifs in endocrine circuits.
M. Raz, D.S. Glass, T. Milo, Y. Korem Kohanim, O. Karin, A. Tendler, A. Mayo, U. Alon.
Preventing plasmid multimer formation in commonly used synthetic biology plasmids.
​A synthetic differentiation circuit in Escherichia coli for suppressing mutant takeover.