Encoding Information and Directing Cell Fate Using Ras/Erk Signaling Dynamics

Abstract

The cells of developing and adult mammalian tissues are tasked with taking in information from their environment (e.g., growth cues, nutrients) and then using that information to make decisions about when and where to execute specific behaviors (e.g., proliferation, migration, differentiation). Hundreds of distinct cell surface receptors sense environmental inputs but, surprisingly, cells transmit this complex information from input to output using fewer than ten signal transduction pathways. This highlights an important question: how do cells accurately transmit complex information using so few ‘wires’? In this thesis, we examine one potential answer by studying cells’ ability to encode information in a language of time-varying or dynamic signaling activity. We focus on the Ras/Erk signaling network, an ideal system because of its pulsatile dynamics, its role as a central driver of proliferation, and the well-established suite of experimental tools for monitoring and controlling its dynamics.

Can we define the types of ‘signals’ generated by the Ras/Erk pathway and causally map their effects on cellular outputs? Here we examine this question at three levels. First, in Chapter 2, we dissect one of the Ras/Erk-regulated processes that allows it to control proliferation using optogenetic and metabolomic approaches. We discovered that extended Ras activation enhances the rate of glucose metabolism by upregulating four key nodes in the glycolytic pathway, one or more of which is consistently upregulated in human cancers. Chapter 3 focuses on the signal transduction process, as we explore how dynamic Ras/Erk signals are regulated and interpreted into proliferative decisions. We performed a drug screen in primary mouse keratinocytes and found multiple distinct classes of drug-altered Erk dynamics. We then used optogenetic manipulation to show that cells make different proliferative decisions in response to each class of drug-altered dynamics. Finally, Chapter 4 zooms in further to focus on the Erk pulse generator itself, showing that pulses arise downstream of receptor-level processes. Our results provide fundamental insights into how pleiotropic signaling networks like Ras/Erk can use the dynamic activity of a single ‘wire’ to transmit information from upstream inputs into distinct cell fate outputs.

Collectively, this thesis draws in equal parts from classic molecular biology, engineering, biochemistry, and quantitative/systems biology to address fundamental scientific questions, from signal processing to emergent properties to cell fate control. We hope this work will inform and provide a framework for future quantitative studies of the ‘language’ of cell signaling.