Molecular Biology Faculty
Jared E. Toettcher
|Toettcher Research Lab|
Lewis Thomas Laboratory, 138-141
Starts: January 2015
Cells live in an information‐rich world, where nutrients, neighboring cells and environmental stresses must each be sensed, processed and responded to appropriately. These cell decisions also matter: we are entering an era where understanding and controlling them could improve therapies based on re‐engineering cell behavior, such as cell fate control for organ regeneration, and help treat diseases that deregulate information flow, like unchecked growth and proliferation in cancer. But although we know the identity of many of the signaling molecules involved in cellular decision making, our understanding of how these molecules work together, especially when integrating many diverse inputs, is still quite primitive. How does the emergent ability to encode and store information arise from protein‐protein interactions? What kind of signals – patterns of protein activity in space and time – are read out by the cell to initiate specific outcomes?
In asking these questions, we are particularly fascinated by a model system – the control of cell proliferation and differentiation downstream of receptor tyrosine kinases (RTKs). RTKs are a large family of cell surface receptors, and different members of the family can control fates as diverse as cell growth, division, survival during stress, or differentiation to terminal states. Surprisingly, RTKs can direct their wide range of responses even though different receptors in the family talk to a highly overlapping set of intracellular signaling pathways. To better understand and control how specific outcomes are encoded, we apply a variety of techniques from cell biology, engineering and synthetic biology.
Harnessing optogenetics to precisely control inputs to cell signaling
Fluorescent reporters have revolutionized our understanding of cellular decision-making by making it possible to observe the levels, activity states, and location of proteins inside living cells. However, in contrast to our ability to precisely measure these cellular outputs, our control over the inputs that can be delivered to cell signaling pathways is still quite limited. One focus of my laboratory is the development and use of optogenetic inputs to cell signaling, particularly the light-gated association of two plant proteins, Phytochrome B and PIF6, which can be ported into a wide variety of cell types and organisms. Unlike small molecules or proteins, which diffuse and may interact with many binding partners, the spatial location and intensity of light can be controlled with extremely high precision. However, these tools are still in their early years. To achieve their full capability, my laboratory will continue engineer light-gated control over new cell signaling processes, and expand the palette of optogenetic tools that can be used in cells.
What pathway combinations and dynamics specify cell fate?
One major function of receptor tyrosine kinase signaling, particularly through fibroblast growth factor receptors (FGFRs), is to control differentiation of pluripotent cells. Using engineered control over two key signaling proteins downstream of receptor tyrosine kinases – the small G protein Ras and the lipid kinase PI3K – we are investigating how the level, duration and spatial organization of signaling activity controls cell differentiation. We picture this process in analogy to a “phase diagram” in physics, where control parameters (temperature and pressure) specify a material’s phase (solid, liquid or gas). By systematically varying pathway activity levels, dynamics and molecular organization, we aim to determine what these control parameters are, and whether the boundaries between different cell fates are as sharp as those between material properties.
How do signaling input-output relationships vary across different cellular contexts?
By combining dynamic inputs and live‐cell reporters, it is possible to directly measure input/output relationships at the single‐cell level with quantitative precision. For instance, we have determined that in fibroblasts, signals delivered to Ras take about 3 minutes to traverse the MAP kinase signaling cascade and activate Erk, and this transmission is equally efficient across a broad range of input levels and timescales. We are interested in extending these approaches to ask whether these commonly reused pathways change input-output relationships in different cellular contexts. Does a T cell, tasked with quickly sampling antigen-presenting cells to identify pathogenic peptides, alter its MAP kinase input-output relationship? What about cancer cells, in which key pathway components are often mutated?
Cancer is in part a disease of signal transmission: pathways that are important to normal cell behavior are “rewired” to generate improper responses. But although advances in genome sequencing have identified a huge number of mutations that can contribute to tumorigenesis, we have very little idea of how these mutations work together to functionally alter cell signaling. A major focus of my lab will be to ask how signal transmission measurements can be used to profile the signaling changes between normal and cancer cells, and infer how network architecture is rewired as a function of mutation.
Toettcher, J.E., Weiner, O.D., and Lim, W.A. "Using optogenetics to interrogate the dynamic control of signal transmission by the Ras/Erk module" Cell 155(6):1422-34 (2013).
Toettcher, J.E., Gong, D., Lim, W.A., and Weiner, O.D. "Light-based feedback for controlling intracellular signaling dynamics." Nature Methods 8, 837-839 (2011).
Toettcher, J.E., Voigt, C.A., Weiner, O.D., and Lim, W.A. "The promise of optogenetics in cell biology: interrogating molecular circuits in space and time." Nature Methods 1, 35-38 (2011).
Toettcher, J.E., Gong, D., Lim, W.A., and Weiner, O.D. "Light control of plasma membrane recruitment using the Phy-PIF system." Methods in Enzymology 497, 409-23 (2011).
Toettcher, J.E., Castillo, A., Tidor, B., and White, J.K. "Oscillator sensitivity analysis in the presence of hidden conservation constraints." Proceedings of the 48th IEEE Design Automation Conference 806-811 (2011).
Toettcher, J.E., Apgar, J.F., Castillo, A.R., Tidor, B., and White, J.K. "Recycling circuit simulation techniques for mass-action biochemical kinetics." Advanced Simulation and Verification of Electronic and Biological Systems, 115-136 (2011).
Toettcher, J.E., Mock, C., Batchelor, E., Loewer, A., and Lahav, G. "A synthetic-natural hybrid oscillator in human cells." Proceedings of the National Academy of Sciences 107, 17047-52 (2010).
Toettcher, J.E., Loewer, A., Ostheimer, G.J., Yaffe, M.B., Tidor, B., and Lahav, G. "Distinct mechanisms act in concert to mediate cell cycle arrest." Proceedings of the National Academy of Sciences 106, 785-90 (2009).
Apgar, J.F., Toettcher, J.E., Endy, D., White, F.M., and Tidor, B. "Stimulus design for model selection and validation in cell signaling." PLoS Computational Biology 4, e30 (2008).
Weinberger, L.S., Burnett, J.C., Toettcher, J.E., Arkin, A.P., and Schaffer, D.V. "Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity." Cell 122, 169-82 (2005).