The regulatory circuits for hysteretic switching in cellular signal transduction pathways

Bistability in cell signalling and its significance in identifying potential drug targets

MOTIVATION

Bistability is one of the salient dynamical features in various all-or-none kinds of decision-making processes. The presence of bistability in a cell signalling network plays a key role in input-output (I/O) relation. Our study is aiming to capture and emphasise the role of motif structure influencing the I/O relation between two nodes in the context of bistability. Here, a model-based analysis is made to investigate the critical conditions responsible for the emergence of different bistable protein-protein interaction (PPI) motifs and their possible applications to find the potential drug targets.

RESULTS

The global sensitivity analysis is used to identify sensitive parameters and their role in maintaining the bistability. Additionally, the bistable switching through hysteresis is explored to develop an understanding of the underlying mechanisms involved in the cell signalling processes, when significant motifs exhibiting bistability have emerged. Further, we elaborate the application of the results by the implication of the emerged PPI motifs to identify potential drug-targets in three cancer networks, which is validated with existing databases. The influence of stochastic perturbations that could hinder desired functionality of any signalling networks is also described here.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Cell memory of epithelial-mesenchymal plasticity in cancer

Fundamental biological processes of cell identity and cell fate determination are controlled by complex regulatory networks. These processes require molecular mechanisms that confer cellular phenotypic memory and state persistence. In this minireview, we will summarize mechanisms of cell memory based on regulatory hysteretic feedback loops and explore epigenetic mechanisms widely represented in nature, with special focus on epithelial-to-mesenchymal plasticity. We will also discuss the functional consequences of cell memory and epithelial-to-mesenchymal plasticity dynamics during development and cancer metastasis.

A positive feedback loop bi-stably activates fibroblasts

Although fibroblasts are dormant in normal tissue, they exhibit explosive activation during wound healing and perpetual activation in pathologic fibrosis and cancer stroma. The key regulatory network controlling these fibroblast dynamics is still unknown. Here, we report that Twist1, a key regulator of cancer-associated fibroblasts, directly upregulates Prrx1, which, in turn, increases the expression of Tenascin-C (TNC). TNC also increases Twist1 expression, consequently forming a Twist1-Prrx1-TNC positive feedback loop (PFL). Systems biology studies reveal that the Twist1-Prrx1-TNC PFL can function as a bistable ON/OFF switch and regulates fibroblast activation. This PFL can be irreversibly activated under pathologic conditions, leading to perpetual fibroblast activation. Sustained activation of the Twist1-Prrx1-TNC PFL reproduces fibrotic nodules similar to idiopathic pulmonary fibrosis in vivo and is implicated in fibrotic disease and cancer stroma. Considering that this PFL is specific to activated fibroblasts, Twist1-Prrx1-TNC PFL may be a fibroblast-specific therapeutic target to deprogram perpetually activated fibroblasts.

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

A critical event in mammalian embryo development is construction of an inner cell mass surrounded by a trophoectoderm (a shell of cells that later form extraembryonic structures). We utilize multi-scale, stochastic modeling to investigate the design principles responsible for robust establishment of these structures. This investigation makes three predictions, each supported by our quantitative imaging. First, stochasticity in the expression of critical genes promotes cell plasticity and has a critical role in accurately organizing the developing mouse blastocyst. Second, asymmetry in the levels of noise variation (expression fluctuation) of Cdx2 and Oct4 provides a means to gain the benefits of noise-mediated plasticity while ameliorating the potentially detrimental effects of stochasticity. Finally, by controlling the timing and pace of cell fate specification, the embryo temporally modulates plasticity and creates a time window during which each cell can continually read its environment and adjusts its fate. These results suggest noise has a crucial role in maintaining cellular plasticity and organizing the blastocyst.

A critical event in mammalian embryo development is construction of a mass of embryonic stem cells surrounded by a distinct shell that later forms the placenta along with other structures. Despite sustained investigation, multiple hypotheses for what is responsible for this organization persist and it remains unclear what is responsible for the robust organization (remarkable ability for embryos to pattern correctly) of these structures. Here, we utilize multi-scale, stochastic modeling along with fluorescence imaging to investigate the factors that contribute to the incredible robustness of this organizational process. Results point to two factors that contribute to this robustness: 1) the timing and pace of cell fate specification and 2) stochastic gene regulatory effects. The former creates a window of time during which each cell can continually read their environment and adjust their gene expressions (and consequently fate) in response to dynamic rearrangements of cells arising from cell divisions and motions. The latter improves cell plasticity, providing the capability for cells to adjust to changes in their local environment. Fluorescence imaging results demonstrate that the magnitude and structure of gene expression variations match those predicted to promote organizational robustness.

The hidden switches underlying RORα-mediated circuits that critically regulate uncontrolled cell proliferation

Prostaglandin E2 (PGE2) is known to have a key role in the development of colorectal cancer, but previous experiments showed its contrasting (i.e. tumor-promoting or tumor-suppressive) roles depending on experimental conditions. To elucidate the mechanisms underlying such contrasting roles of PGE2 in tumorigenesis, we investigated all the previous experiments and found a new signal transduction pathway mediated by retinoic acid receptor-related orphan receptor (ROR)α, in which PGE2/PKCα-dependent phosphorylation of RORα attenuates Wnt target gene expression in colon cancer cells. From mathematical simulations combined with biochemical experimentation, we revealed that RORα induces a biphasic response of Wnt target genes to PGE2 stimulation through a regulatory switch formed by an incoherent feedforward loop, which provides a mechanistic explanation on the contrasting roles of PGE2 observed in previous experiments. More interestingly, we found that RORα constitutes another regulatory switch formed by coupled positive and negative feedback loops, which regulates the hysteretic response of Wnt signaling and eventually converts a proliferative cellular state into an anti-proliferative state in a very delicate way. Our results indicate that RORα is the key regulator at the center of these hidden switches that critically regulate cancer cell proliferation and thereby being a promising anti-cancer therapeutic target.

Noise attenuation in the ON and OFF states of biological switches

Biological switches must sense changes in signal concentration and at the same time buffer against signal noise. While many studies have focused on the response of switching systems to noise in the ON state, how systems buffer noise at both ON and OFF states is poorly understood. Through analytical and computational approaches, we find that switching systems require different dynamics at the OFF state than at the ON state in order to have good noise buffering capability. Specifically, we introduce a quantity called the input-associated Signed Activation Time (iSAT) that concisely captures an intrinsic temporal property at either the ON or OFF state. We discover a trade-off between achieving good noise buffering in the ON versus the OFF states: a large iSAT corresponds to noise amplification in the OFF state in contrast to noise buffering in the ON state. To search for biological circuits that can buffer noise in both ON and OFF states, we systematically analyze all three-node circuits and identify mutual activation as a central motif. We also study connections among signal sensitivity, iSAT, and noise amplification. We find that a large iSAT at the ON state maintains signaling sensitivity while minimizing noise propagation. Taken together, the analysis of iSATs helps reveal the noise properties of biological networks and should aid in the design of robust switches that can both repress noise at the OFF state and maintain a reliable ON state.