Abstract 4925: The natural enzyme sequestration in signaling cascades provides inherent opportunities for off-target effects induced by kinase inhibitors

Off-target effects from targeted therapies are often attributed to cross-talk, which usually refers to inter-pathway molecular interactions that occur because of explicit regulatory feedback connections between two pathways. Recent experimental and theoretical studies have demonstrated, however, that covalently modified cascades naturally exhibit bidirectional signal propagation via a phenomenon termed retroactivity. This phenomenon arises due to enzyme sequestration where each cycle is coupled, not only to the next cycle, but also to the previous cycle. While retroactivity occurs naturally in covalently modified cascades, signaling pathways likely evolved to propagate information in a downstream manner. An important consequence of retroactivity, however, is that a downstream perturbation can induce an upstream response without the presence of regulatory feedback connections. We hypothesize that kinase inhibitors can produce off-target effects as a consequence of retroactivity alone via the following mechanism: a signal travels upstream from the site of a downstream perturbation through retroactivity and, upon reaching a shared upstream component, is delivered to an independent parallel pathway. To test the hypothesis we used a computational model to simulate the targeted inhibition of a specific kinase in a series signaling networks using physiologically and therapeutically relevant ranges for all parameters. Surprisingly, our results suggest that an off-target effect due to retroactive signaling is more likely when the first cycle in a non-inhibited cascade is “off” and not consuming large amounts of a shared up-stream activator. Our results also suggest that the kinetics governing covalently modified cycles in a cascade are more important for propagating an upstream off-target effect than the binding affinity of the drug to the targeted protein, which is a commonly optimized property in drug development. Finally, our results suggest that a single mutation has the capacity to produce a large spontaneous off-target effect without any direct regulatory connections between the targeted protein and the effected protein. Together, our results suggest that retroactivity may play an important role in the dysregulated signaling networks of cancer cells as well as the cellular response to targeted therapies. These findings have important implications for somatic evolution in cancer and the onset of therapeutic resistance, which has been widely reported for many targeted cancer therapeutics, including kinase inhibitors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4925. doi:1538-7445.AM2012-4925

Abstract 4907: Elucidating the role of retroactive signaling and kinase inhibitors on off-target drug effects

The primary objective of targeted cancer therapies is to modulate cancer progression by perturbing specific molecules involved in aberrant proliferation and invasion. Kinase inhibitors are targeted therapies which are designed to interfere with a specific kinase molecule in a dysregulated oncogenic signaling cascade. While extremely promising as anti-cancer agents, such inhibitors may have undesirable off-target effects, whether by non-specific interactions or by effects from pathway cross-talk. We have shown in published experimental and theoretical work that covalently modified signaling cascades naturally exhibit bidirectional signal propagation. This phenomenon is termed retroactivity and challenges the widespread notion that information in cascades only flows from the cell surface to the nucleus. Previous work has demonstrated that increasing the concentration of a phosphatase in the terminal cycle of a covalently modified cascade may result in a measurable decrease in the concentration of the previous cycle's activated kinase. Thus, a downstream perturbation in a signaling cascade can produce a reverse (or retroactive) response without the need for direct negative feedback connections. This led us to hypothesize that the use of an inhibitory drug in a signaling network may cause an upstream off-target effect simply by inhibiting the activation or deactivation of a downstream kinase. To test the hypothesis that retroactivity contributes to off-target effects, we extended our previous work to a computational model that tested a series of signaling networks. The objective of our approach was two-fold: (1) to probe the effect of retroactivity on a kinase inhibitor in a signaling network and (2) to test whether retroactivity is likely to produce a measurable off-target effect under physiologically realistic conditions. Specifically, our model simulates the targeted inhibition of an activated kinase in a series of multi-cycle networks. The results of our work indicate that at physiologically and therapeutically relevant concentrations, a targeted inhibitor may induce a measurable off-target effect via retroactivity. We also performed local sensitivity analyses to predict the kinetic parameters that most affect the off-target response. Surprisingly, the drug disassociation constant is predicted to have very little effect while parameters such as the enzyme saturation and maximum velocity of some cycles are predicted to be very important. A proper characterization of a pathway's structure is important for identifying which protein in the pathway represents the optimal drug target as well as what concentration of the targeted therapy is likely to modulate the pathway in the manner desired. We believe our results support the position that such characterizations should consider the role of retroactivity as a source of a potential off-target effects by kinase inhibitors.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4907. doi:10.1158/1538-7445.AM2011-4907

A hidden feedback in signaling cascades is revealed

Cycles involving covalent modification of proteins are key components of the intracellular signaling machinery. Each cycle is comprised of two interconvertable forms of a particular protein. A classic signaling pathway is structured by a chain or cascade of basic cycle units in such a way that the activated protein in one cycle promotes the activation of the next protein in the chain, and so on. Starting from a mechanistic kinetic description and using a careful perturbation analysis, we have derived, to our knowledge for the first time, a consistent approximation of the chain with one variable per cycle. The model we derive is distinct from the one that has been in use in the literature for several years, which is a phenomenological extension of the Goldbeter-Koshland biochemical switch. Even though much has been done regarding the mathematical modeling of these systems, our contribution fills a gap between existing models and, in doing so, we have unveiled critical new properties of this type of signaling cascades. A key feature of our new model is that a negative feedback emerges naturally, exerted between each cycle and its predecessor. Due to this negative feedback, the system displays damped temporal oscillations under constant stimulation and, most important, propagates perturbations both forwards and backwards. This last attribute challenges the widespread notion of unidirectionality in signaling cascades. Concrete examples of applications to MAPK cascades are discussed. All these properties are shared by the complete mechanistic description and our simplified model, but not by previously derived phenomenological models of signaling cascades.

Transmitting a signal by amplitude modulation in a chaotic network

We discuss the ability of a model of network with nonlinear units and chaotic dynamics to transmit signals, on the basis of a linear response theory developed by Ruelle [D. Ruelle, J. Stat. Phys. 95, 393 (1999)] for dissipative systems. We discuss in particular how the dynamics may interfere with the graph topology to produce an effective transmission network, whose topology depends on the signal, and cannot be directly read on the "wired" network. Then, we show examples where, with a suitable choice of the carrier frequency (resonance), one can transmit a signal from a node to another one by amplitude modulation, in spite of chaos. Also, we give an example where a signal, transmitted to any node via different paths, can only be recovered by a couple of specific nodes. This opens up the possibility for encoding data in a way such that the recovery of the signal requires the knowledge of the carrier frequency and can be performed only at some specific node.

Stable resonances and signal propagation in a chaotic network of coupled units

We apply the linear response theory developed by Ruelle [J. Stat. Phys. 95, 393 (1999)] to analyze how a periodic signal of weak amplitude, superimposed upon a chaotic background, is transmitted in a network of nonlinearly interacting units. We numerically compute the complex susceptibility and show the existence of specific poles (stable resonances) corresponding to the response to perturbations transverse to the attractor. Contrary to the poles of correlation functions they depend on the pair emitting-receiving units. This dynamic differentiation, induced by nonlinearities, exhibits the different ability that units have to transmit a signal in this network.