The tyrosine phosphatase SHP2 increases robustness and information transfer within IL-6-induced JAK/STAT signalling.

BACKGROUND: Cell-to-cell heterogeneity is an inherent feature of multicellular organisms and is central in all physiological and pathophysiological processes including cellular signal transduction. The cytokine IL-6 is an essential mediator of pro- and anti-inflammatory processes. Dysregulated IL-6-induced intracellular JAK/STAT signalling is associated with severe inflammatory and proliferative diseases. Under physiological conditions JAK/STAT signalling is rigorously controlled and timely orchestrated by regulatory mechanisms such as expression of the feedback-inhibitor SOCS3 and activation of the protein-tyrosine phosphatase SHP2 (PTPN11). Interestingly, the function of negative regulators seems not to be restricted to controlling the strength and timely orchestration of IL-6-induced STAT3 activation. Exemplarily, SOCS3 increases robustness of late IL-6-induced STAT3 activation against heterogenous STAT3 expression and reduces the amount of information transferred through JAK/STAT signalling. METHODS: Here we use multiplexed single-cell analyses and information theoretic approaches to clarify whether also SHP2 contributes to robustness of STAT3 activation and whether SHP2 affects the amount of information transferred through IL-6-induced JAK/STAT signalling. RESULTS: SHP2 increases robustness of both basal, cytokine-independent STAT3 activation and early IL-6-induced STAT3 activation against differential STAT3 expression. However, SHP2 does not affect robustness of late IL-6-induced STAT3 activation. In contrast to SOCS3, SHP2 increases the amount of information transferred through IL-6-induced JAK/STAT signalling, probably by reducing cytokine-independent STAT3 activation and thereby increasing sensitivity of the cells. These effects are independent of SHP2-dependent MAPK activation. CONCLUSION: In summary, the results of this study extend our knowledge of the functions of SHP2 in IL-6-induced JAK/STAT signalling. SHP2 is not only a repressor of basal and cytokine-induced STAT3 activity, but also ensures robustness and transmission of information. Plain English summary Cells within a multicellular organism communicate with each other to exchange information about the environment. Communication between cells is facilitated by soluble molecules that transmit information from one cell to the other. Cytokines such as interleukin-6 are important soluble mediators that are secreted when an organism is faced with infections or inflammation. Secreted cytokines bind to receptors within the membrane of their target cells. This binding induces activation of an intracellular cascade of reactions called signal transduction, which leads to cellular responses. An important example of intracellular signal transduction is JAK/STAT signalling. In healthy organisms signalling is controlled and timed by regulatory mechanisms, whose activation results in a controlled shutdown of signalling pathways. Interestingly, not all cells within an organism are identical. They differ in the amount of proteins involved in signal transduction, such as STAT3. These differences shape cellular communication and responses to intracellular signalling. Here, we show that an important negative regulatory protein called SHP2 (or PTPN11) is not only responsible for shutting down signalling, but also for steering signalling in heterogeneous cell populations. SHP2 increases robustness of STAT3 activation against variable STAT3 amounts in individual cells. Additionally, it increases the amount of information transferred through JAK/STAT signalling by increasing the dynamic range of pathway activation in heterogeneous cell populations. This is an amazing new function of negative regulatory proteins that contributes to communication in heterogeneous multicellular organisms in health and disease. Video Abstract.

Information-theoretic analysis of multivariate single-cell signaling responses.

Mathematical methods of information theory appear to provide a useful language to describe how stimuli are encoded in activities of signaling effectors. Exploring the information-theoretic perspective, however, remains conceptually, experimentally and computationally challenging. Specifically, existing computational tools enable efficient analysis of relatively simple systems, usually with one input and output only. Moreover, their robust and readily applicable implementations are missing. Here, we propose a novel algorithm, SLEMI-statistical learning based estimation of mutual information, to analyze signaling systems with high-dimensional outputs and a large number of input values. Our approach is efficient in terms of computational time as well as sample size needed for accurate estimation. Analysis of the NF-κB single-cell signaling responses to TNF-α reveals that NF-κB signaling dynamics improves discrimination of high concentrations of TNF-α with a relatively modest impact on discrimination of low concentrations. Provided R-package allows the approach to be used by computational biologists with only elementary knowledge of information theory.

StochDecomp--Matlab package for noise decomposition in stochastic biochemical systems.

MOTIVATION: Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with non-trivial insights into the origins of stochasticity, in total, however, they constitute a patchwork of different theoretical analyses. RESULTS: Here we present a flexible and widely applicable noise decomposition tool that allows us to calculate contributions of individual reactions to the total variability of a system's output. With the package it is, therefore, possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that the noise contributions resulting from individual reactions can be inferred from data experimental data along with Bayesian parameter inference. The method is based on the linear noise approximation, which is assumed to provide a reasonable representation of analyzed systems. AVAILABILITY AND IMPLEMENTATION: http://sourceforge.net/p/stochdecomp/

Validation and Reliability of Polish Version of the Reflux Symptoms Index and Reflux Finding Score.

(1) Background: To confirm the credibility, consistency, and replicability of the Polish versions of the Reflux Symptoms Index (PL-RSI) and the Reflux Finding Score (PL-RFS). (2) Methods: The translation followed the WHO recommendations. The study group included 100 volunteers (age 15−87) with hoarseness and pharyngolaryngeal complaints. The control group comprised 55 healthy volunteers (age 20−75). Study participants completed the PL-RSI; then, two independent otolaryngologists completed the PL-RFS based on pharyngeal videostroboscopy. Questionnaires were repeated after 7 days, with no treatment before the second round. Additionally, patients underwent 24 h pH-metry. The control group had a single round of questionnaires followed by pH-metry. (3) Results: The PL-RSI is consistent, reliable (Cronbach's alpha 0.77−0.83; test−retest reliability 0.83), and significantly correlated with other patient-filled tools (p < 0.001). The PL-RFS intra-rater reliability is 0.84−0.91, and inter-rater is 0.88. Both questionnaires strongly correlate with pH-metry (PL-RSI upright Ryan Score 0.35, PL-RFS­0.60). Both clearly distinguish (i) healthy from persons with voice disorders, but without acid LPR (p < 0.0001), and (ii) within patient group between subjects with and without acid LPR (p = 0.0002). (4) Conclusions: The PL-RSI and PL-RFS are reliable and can be recommended to Polish-speaking otolaryngologists. Our findings confirm the role of country-specific factors in RSI results and that practitioners should always use a proper control group.

Diagnosis of laryngopharyngeal reflux in children with voice disorders using 24-hour pharyngeal pH monitoring.

OBJECTIVES: The aim of this study was to assess the usefulness of 24-h pharyngeal pH monitoring in the diagnosis of laryngopharyngeal reflux (LPR) in children with voice disorders. METHODS: The study was conducted on 68 children aged 3-18 years old. In all cases, pH monitoring was successful; no child removed the probe from the nasal cavity or reported discomfort or other complaints. The following definitions were adopted: LPR in the upright position if Ryan Score upright >9.41; LPR in the supine position if there was at least one supine episode below pH 5.0 (equal to a Ryan Score supine >2.91). RESULTS: In 43 children (63%), vocal fold edema was strongly related to recorded reflux episodes, especially in the upright position. In 18 children (26%), vocal nodules were observed, but their occurrence did not significantly affect the Ryan Score, either upright or supine. The selected potential LPR markers were significantly correlated to all the pH monitoring variables and individual elements on the Reflux Symptoms Index and the Reflux Finding Score questionnaire. CONCLUSION: Our findings indicate that, together with vocal fold edema, laryngeal edema and posterior commissure mucosal hypertrophy are important determinants of paediatric LPR. In fact, if LPR is suspected in a child, 24-h pharyngeal pH monitoring appears to be a valuable and welltolerated diagnostic tool. Vocal fold edema observed in laryngeal endoscopy can be considered a probable sign of LPR. The Reflux Finding Score appears to be helpful in diagnosing LPR in children, especially if a cut-off value of 4/5 is adopted.

Robustness and Information Transfer within IL-6-induced JAK/STAT Signalling.

Cellular communication via intracellular signalling pathways is crucial. Expression and activation of signalling proteins is heterogenous between isogenic cells of the same cell-type. However, mechanisms evolved to enable sufficient communication and to ensure cellular functions. We use information theory to clarify mechanisms facilitating IL-6-induced JAK/STAT signalling despite cell-to-cell variability. We show that different mechanisms enabling robustness against variability complement each other. Early STAT3 activation is robust as long as cytokine concentrations are low. Robustness at high cytokine concentrations is ensured by high STAT3 expression or serine phosphorylation. Later the feedback-inhibitor SOCS3 increases robustness. Channel Capacity of JAK/STAT signalling is limited by cell-to-cell variability in STAT3 expression and is affected by the same mechanisms governing robustness. Increasing STAT3 amount increases Channel Capacity and robustness, whereas increasing STAT3 tyrosine phosphorylation reduces robustness but increases Channel Capacity. In summary, we elucidate mechanisms preventing dysregulated signalling by enabling reliable JAK/STAT signalling despite cell-to-cell heterogeneity.

An information-theoretic framework for deciphering pleiotropic and noisy biochemical signaling.

Many components of signaling pathways are functionally pleiotropic, and signaling responses are marked with substantial cell-to-cell heterogeneity. Therefore, biochemical descriptions of signaling require quantitative support to explain how complex stimuli (inputs) are encoded in distinct activities of pathways effectors (outputs). A unique perspective of information theory cannot be fully utilized due to lack of modeling tools that account for the complexity of biochemical signaling, specifically for multiple inputs and outputs. Here, we develop a modeling framework of information theory that allows for efficient analysis of models with multiple inputs and outputs; accounts for temporal dynamics of signaling; enables analysis of how signals flow through shared network components; and is not restricted by limited variability of responses. The framework allows us to explain how identity and quantity of type I and type III interferon variants could be recognized by cells despite activating the same signaling effectors.

Signaling pathway activation drift during aging: Hutchinson-Gilford Progeria Syndrome fibroblasts are comparable to normal middle-age and old-age cells.

For the past several decades, research in understanding the molecular basis of human aging has progressed significantly with the analysis of premature aging syndromes. Progerin, an altered form of lamin A, has been identified as the cause of premature aging in Hutchinson-Gilford Progeria Syndrome (HGPS), and may be a contributing causative factor in normal aging. However, the question of whether HGPS actually recapitulates the normal aging process at the cellular and organismal level, or simply mimics the aging phenotype is widely debated. In the present study we analyzed publicly available microarray datasets for fibroblasts undergoing cellular aging in culture, as well as fibroblasts derived from young, middle-age, and old-age individuals, and patients with HGPS. Using GeroScope pathway analysis and drug discovery platform we analyzed the activation states of 65 major cellular signaling pathways. Our analysis reveals that signaling pathway activation states in cells derived from chronologically young patients with HGPS strongly resemble cells taken from normal middle-aged and old individuals. This clearly indicates that HGPS may truly represent accelerated aging, rather than being just a simulacrum. Our data also points to potential pathways that could be targeted to develop drugs and drug combinations for both HGPS and normal aging.