Research

Cells make decisions by decoding complex signaling environments. We dissect this code with precise optogenetic tools to better understand normal cell function and disease states, and to uncover new methods for cellular control.

 
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Cellular Optogenetics

Our lab specializes in optogenetic technologies, which let us control cellular events in real-time using light.

Why do we do this? Cells sense their complex environments through dynamic activation of intracellular signals, which instruct cells how to behave. However, we have a limited understanding of how cells respond to such signals because the traditional tools for probing cell signaling (drugs, genetic manipulation) are static and difficult to manipulate. Light-activation lets us arbitrarily define the intensity, timing, and location of signals within a cell, allowing us to better mimic a cell’s dynamic signaling environment and to systematically explore the effects of these important signal parameters.

How do we do this? We engineer optogenetic proteins by borrowing from plants, which evolved light-sensitive proteins to sense and respond to sunlight. We use protein engineering to generate new molecular tools that plug in to important mammalian signaling nodes, giving us optical control of those nodes and networks.

 


Information processing through intracellular signaling pathways

Decades of work have successfully mapped out the networks of molecules that cells use to make decisions. And yet, these molecules represent only the hardware of the cell, like the transistors in a computer.  We are interested in understanding the cellular software, or how signals flow across molecular networks to give proper cell function. How does a signal’s intensity or fluctuations impact the cell? How do cells distinguish meaningful signal dynamics from molecular noise? How do cells integrate information from multiple pathways simultaneously? We use optogenetics to specifically and precisely modulate key signaling nodes (e.g. Ras or b-catenin) and interrogate the response at multiple levels of cellular decision-making.

 A fluorescent reporter of Erk activity (Erk-KTR) reveals Erk pathway dynamics in 3T3 cells.

A fluorescent reporter of Erk activity (Erk-KTR) reveals Erk pathway dynamics in 3T3 cells.


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Reverse engineering stem cell fate decisions

Successful regenerative medicine therapies will require understanding how stem cells reliably differentiate into desired cell types. Our high throughput optogenetic tools enable a systematic approach, where we can rapidly map cellular outputs to a large input space of important differentiations signals. This will allow us to uncover both 1) signal parameters for effective stem cell manipulation, and 2) functional insights into the underlying molecular circuitry. Beyond single cells, we also apply these approaches within cell collectives including organoid models.

 


Signal (mis)perception in disease

Cancer cell growth is not strictly a cell autonomous disease, but rather can depend on extrinsic cues from the cancer microenvironment. We explore the hypothesis that oncogenes may not simply "switch on" proliferative signaling, but rather can functionally change a cell’s interpretation – or perception – of its environment, leading to pathological cell decisions like hyperproliferation.  Our previous work showed that particular cancer cells can have altered dynamic responses in growth regulatory networks, and this altered response can drive inappropriate cell cycle entry. We explore the prevalence of signal misperception in cancer to better understand oncogenesis and to ultimately develop new disease metrics and treatment strategies.

 Certain cancer cells may misinterpret dynamic signals to inappropriately proliferate

Certain cancer cells may misinterpret dynamic signals to inappropriately proliferate


 Cryptochrome2 clusters and dissociates in response to light 

Cryptochrome2 clusters and dissociates in response to light 

Engineering new molecular tools

Our group innovates new molecular inputs (optogenetic probes) and outputs (reporters) to explore how different pathways and behaviors regulate cellular function.


Instrumentation

There is a need for hardware to enable high-throughput and reproducible optogenetic experiments.   Our lab develops custom devices and protocols to enable systematic, high-throughput optogenetic experiments compatible with standard tissue culture workflows.  The optoPlate-96 gives us fully programmable control of up to 3 colors in individual wells in 96- and 384-well microplate formats. These devices are adaptable for use either in standard cell culture incubators or under a microscope.  We freely share our device designs with the scientific community (publication and website coming soon!) and we welcome collaboration with colleagues who want to use these devices in their own work.

 The optoPlate-96

The optoPlate-96