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Publications by Eduardo D. Sontag in year 2020
Articles in journal or book chapters
  1. M.A. Al-Radhawi and E.D. Sontag. Analysis of a reduced model of epithelial-mesenchymal fate determination in cancer metastasis as a singularly-perturbed monotone system. In C.A. Beattie, P. Benner, M. Embree, S. Gugercin, and S. Lefteriu, editors, Realization and Model Reduction of Dynamical Systems. Springer-Verlag, 2020. Note: To appear. See preprint in arXiv:1910.11311. [PDF] Keyword(s): epithelial-mesenchymal transition, miRNA, singular perturbations, monotone systems, oncology, cancer, metastasis, chemical reaction networks, systems biology.
    Abstract:
    Metastasis can occur after malignant cells transition from the epithelial phenotype to the mesenchymal phenotype. This transformation allows cells to migrate via the circulatory system and subsequently settle in distant organs after undergoing the reverse transition. The core gene regulatory network controlling these transitions consists of a system made up of coupled SNAIL/miRNA-34 and ZEB1/miRNA-200 subsystems. In this work, we formulate a mathematical model and analyze its long-term behavior. We start by developing a detailed reaction network with 24 state variables. Assuming fast promoter and mRNA kinetics, we then show how to reduce our model to a monotone four-dimensional system. For the reduced system, monotone dynamical systems theory can be used to prove generic convergence to the set of equilibria for all bounded trajectories. The theory does not apply to the full model, which is not monotone, but we briefly discuss results for singularly-perturbed monotone systems that provide a tool to extend convergence results from reduced to full systems, under appropriate time separation assumptions.


  2. E.D. Sontag. Input-to-State Stability. In J. Baillieul and T. Samad, editors, Encyclopedia of Systems and Control, pages 1-9. Springer-Verlag, 2020. [PDF] Keyword(s): input to state stability, integral input to state stability, iISS, ISS, input to output stability.
    Abstract:
    The notion of input to state stability (ISS) qualitatively describes stability of the mapping from initial states and inputs to internal states (and more generally outputs). This encyclopedia-style article entry gives a brief introduction to the definition of ISS and a discussion of equivalent characterizations. It is an update of the article in the 2015 edition, including additional citations to recent PDE work.


  3. E.D. Sontag. Scale-invariance in biological sensing. In J. Baillieul and T. Samad, editors, Encyclopedia of Systems and Control, pages S1-. Springer-Verlag, 2020. [PDF] [doi:10.1007/978-1-4471-5102-9_100090-1] Keyword(s): adaptation, biological adaptation, perfect adaptation, fold-change detection.
    Abstract:
    The phenomenon of fold-change detection, or scale-invariance, is exhibited by a variety of sensory systems, in both bacterial and eukaryotic signaling pathways. This encyclopedia-style article gives a brief introduction to the subject.


  4. D.K. Agrawal, E.M. Dolan, N.E. Hernandez, K.M. Blacklock, S.D. Khare, and E.D. Sontag. Mathematical models of protease-based enzymatic biosensors. ACS Synthetic Biology, 9:198-208, 2020. [PDF] Keyword(s): synthetic biology, protease-based circuits, enzymatic circuits, systems biology, Boolean circuits.
    Abstract:
    An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.


  5. M.A. Al-Radhawi, D. Angeli, and E.D. Sontag. A computational framework for a Lyapunov-enabled analysis of biochemical reaction networks. PLoS Computational Biology, pp 16(2): e1007681, 2020. [PDF] Keyword(s): Lyapunov functions, stability, chemical networks, chemical rection networks, systems biology.
    Abstract:
    This paper deals with the analysis of the dynamics of chemical reaction networks, developing a theoretical framework based only on graphical knowledge and applying regardless of the particular form of kinetics. It paper introduces a class of networks that are "structurally (mono) attractive", by which we mean that they are incapable of exhibiting multiple steady states, oscillation, or chaos by the virtue of their reaction graphs. These networks are characterized by the existence of a universal energy-like function which we call a Robust Lyapunov function (RLF). To find such functions, a finite set of rank-one linear systems is introduced, which form the extremals of a linear convex cone. The problem is then reduced to that of finding a common Lyapunov function for this set of extremals. Based on this characterization, a computational package, Lyapunov-Enabled Analysis of Reaction Networks (LEARN), is provided that constructs such functions or rules out their existence. An extensive study of biochemical networks demonstrates that LEARN offers a new unified framework. We study basic motifs, three-body binding, and transcriptional networks. We focus on cellular signalling networks including various post-translational modification cascades, phosphotransfer and phosphorelay networks, T-cell kinetic proofreading, ERK signaling, and the Ribosome Flow Model.


  6. M. Ali Al-Radhawi, A.P. Tran, E. Ernst, T. Chen, C.A. Voigt, and E.D. Sontag. Distributed implementation of Boolean functions by transcriptional synthetic circuits. ACS Synthetic Biology, pp A-P, 2020. [PDF] [doi:10.1021/acssynbio.0c00228] Keyword(s): synthetic biology, transcriptional networks, gene networks, boolean circuits, boolean gates.
    Abstract:
    Starting in the early 2000s, sophisticated technologies have been developed for the rational construction of synthetic genetic networks that implement specified logical functionalities. Despite impressive progress, however, the scaling necessary in order to achieve greater computational power has been hampered by many constraints, including repressor toxicity and the lack of large sets of mutually-orthogonal repressors. As a consequence, a typical circuit contains no more than roughly seven repressor-based gates per cell. A possible way around this scalability problem is to distribute the computation among multiple cell types, which communicate among themselves using diffusible small molecules (DSMs) and each of which implements a small sub-circuit. Examples of DSMs are those employed by quorum sensing systems in bacteria. This paper focuses on systematic ways to implement this distributed approach, in the context of the evaluation of arbitrary Boolean functions. The unique characteristics of genetic circuits and the properties of DSMs require the development of new Boolean synthesis methods, distinct from those classically used in electronic circuit design. In this work, we propose a fast algorithm to synthesize distributed realizations for any Boolean function, under constraints on the number of gates per cell and the number of orthogonal DSMs. The method is based on an exact synthesis algorithm to find the minimal circuit per cell, which in turn allows us to build an extensive database of Boolean functions up to a given number of inputs. For concreteness, we will specifically focus on circuits of up to 4 inputs, which might represent, for example, two chemical inducers and two light inputs at different frequencies. Our method shows that, with a constraint of no more than seven gates per cell, the use of a single DSM increases the total number of realizable circuits by at least 7.58-fold compared to centralized computation. Moreover, when allowing two DSM's, one can realize 99.995\% of all possible 4-input Boolean functions, still with at most 7 gates per cell. The methodology introduced here can be readily adapted to complement recent genetic circuit design automation software.


  7. D. Angeli, M.A. Al-Radhawi, and E.D. Sontag. A robust Lyapunov criterion for non-oscillatory behaviors in biological interaction networks. 2020. Note: Submitted. Preprint in arXiv.2009.10702.
    Abstract:
    We introduce the notion of non-oscillation, propose a constructive method for its robust verification, and study its application to biological interaction networks (also known as, chemical reaction networks). We begin by revisiting Muldowney's result on non-existence of periodic solutions based on the study of the variational system of the second additive compound of the Jacobian of a nonlinear system. We show that exponential stability of the latter rules out limit cycles, quasi-periodic solutions, and broad classes of oscillatory behavior. We focus then on nonlinear equations arising in biological interaction networks with general kinetics, and we show that the dynamics of the aforementioned variational system can be embedded in a linear differential inclusion. We then propose algorithms for constructing piecewise linear Lyapunov functions to certify global robust non-oscillatory behavior. Finally, we apply our techniques to study several regulated enzymatic cycles where available methods are not able to provide any information about their qualitative global behavior.


  8. T. Chen, M. Ali Al-Radhawi, and E.D. Sontag. A mathematical model exhibiting the effect of DNA methylation on the stability boundary in cell-fate networks. Epigenetics, 15, 2020. Note: PMID: 32842865. [PDF] [doi:10.1080/15592294.2020.1805686] Keyword(s): methylation, differentiation, epigenetics, pluripotent cells, gene regulatory networks, bistability, bistability.
    Abstract:
    Cell-fate networks are traditionally studied within the framework of gene regulatory networks. This paradigm considers only interactions of genes through expressed transcription factors and does not incorporate chromatin modification processes. This paper introduces a mathematical model that seamlessly combines gene regulatory networks and DNA methylation, with the goal of quantitatively characterizing the contribution of epigenetic regulation to gene silencing. The ``Basin of Attraction percentage'' is introduced as a metric to quantify gene silencing abilities. As a case study, a computational and theoretical analysis is carried out for a model of the pluripotent stem cell circuit as well as a simplified self-activating gene model. The results confirm that the methodology quantitatively captures the key role that methylation plays in enhancing the stability of the silenced gene state.


  9. J Gevertz, J.M. Greene, C Hixahuary Sanchez Tapia, and E D Sontag. A novel COVID-19 epidemiological model with explicit susceptible and asymptomatic isolation compartments reveals unexpected consequences of timing social distancing. Journal of Theoretical Biology, 2020. Note: Under minor revision. Preprint in medRxiv. [WWW]
    Abstract:
    Motivated by the current COVID-19 epidemic, this work introduces an epidemiological model in which separate compartments are used for susceptible and asymptomatic "socially distant" populations. Distancing directives are represented by rates of flow into these compartments, as well as by a reduction in contacts that lessens disease transmission. The dynamical behavior of this system is analyzed, under various different rate control strategies, and the sensitivity of the basic reproduction number to various parameters is studied. One of the striking features of this model is the existence of a critical implementation delay in issuing separation mandates: while a delay of about four weeks does not have an appreciable effect, issuing mandates after this critical time results in a far greater incidence of infection. In other words, there is a nontrivial but tight "window of opportunity" for commencing social distancing. Different relaxation strategies are also simulated, with surprising results. Periodic relaxation policies suggest a schedule which may significantly inhibit peak infective load, but that this schedule is very sensitive to parameter values and the schedule{ extquoteright}s frequency. Further, we considered the impact of steadily reducing social distancing measures over time. We find that a too-sudden reopening of society may negate the progress achieved under initial distancing guidelines, if not carefully designed.


  10. J. M. Greene, C. Sanchez-Tapia, and E.D. Sontag. Mathematical details on a cancer resistance model. Frontiers in Bioengineering and Biotechnology, 8:501: 1-27, 2020. [PDF] [doi:10.3389/fbioe.2020.00501] Keyword(s): resistance, chemotherapy, phenotype, optimal control, singular controls, cancer, oncology.
    Abstract:
    One of the most important factors limiting the success of chemotherapy in cancer treatment is the phenomenon of drug resistance. We have recently introduced a framework for quantifying the effects of induced and non-induced resistance to cancer chemotherapy. In this work, we expound on the details relating to an optimal control problem outlined in our previous paper (Greene et al., 2018). The control structure is precisely characterized as a concatenation of bang-bang and path-constrained arcs via the Pontryagin Maximum Principle and differential Lie algebraic techniques. A structural identifiability analysis is also presented, demonstrating that patient-specific parameters may be measured and thus utilized in the design of optimal therapies prior to the commencement of therapy. For completeness, a detailed analysis of existence results is also included.


  11. H. Hong, J. Kim, M.A. Al-Radhawi, E.D. Sontag, and J. K. Kim. Derivation of stationary distributions of biochemical reaction networks via structure transformation. 2020. Note: Submitted.Keyword(s): stationary distribution, chemical reaction networks, network translation, biochemical reaction networks, chemical master equation, stochastic, probabilistic.
    Abstract:
    The long-term behaviors of biochemical reaction networks (BRNs) are described by steady states in deterministic models, and stationary distributions in stochastic models. Unlike deterministic steady states, the stationary distributions capturing inherent fluctuations of reactions are extremely difficult to derive analytically. Here, we develop a method for deriving stationary distributions from deterministic steady states by translating given BRNs to have a special network structure. Specifically, we merge and shift nodes and edges so as to make the deterministic steady states complex balanced, i.e., in- and out-flows of each node are equal. Then, using the complex balanced steady states, the stationary distributions of various autophosphorylation and toggle switch systems are derived. This greatly extends a class of BRNs for which stationary distributions can be analytically derived.


  12. K. Johnson, G. Howard, D. Morgan, E. Brenner, A. Gardner, R. Durrett, W. Mo, A. Al'Khafaji, E.D. Sontag, A. Jarrett, T. Yankeelov, and A. Brock. Integrating transcriptomics and bulk time course data into a mathematical framework to describe and predict therapeutic resistance in cancer. Physical Biology, 2020. Note: To appear. Keyword(s): oncology, cancer, chemoresistance, resistance, intratumor heterogeneity, population dynamics, DNA barcoding, evolution.
    Abstract:
    The development of resistance to chemotherapy is a major cause of treatment failure in cancer. Intratumoral heterogeneity and phenotypic plasticity play a significant role in therapeutic resistance. Individual cell measurements such as flow and mass cytometry and single cell RNA sequencing (scRNA-seq) have been used to capture and analyze this cell variability. In parallel, longitudinal treatment-response data is routinely employed in order to calibrate mechanistic mathematical models of heterogeneous subpopulations of cancer cells viewed as compartments with differential growth rates and drug sensitivities. This work combines both approaches: single cell clonally-resolved transcriptome datasets (scRNA-seq, tagging individual cells with unique barcodes that are integrated into the genome and expressed as sgRNA's) and longitudinal treatment response data, to fit a mechanistic mathematical model of drug resistance dynamics for a MDA-MB-231 breast cancer cell line. The explicit inclusion of the transcriptomic information in the parameter estimation is critical for identification of the model parameters and enables accurate prediction of new treatment regimens.


  13. J. Miller, M.A. Al-Radhawi, and E.D. Sontag. Mediating ribosomal competition by splitting pools. 2020. Note: Submitted. Preprint in arXiv.2009.00539. Keyword(s): systems biology, synthetic biology, ribosomes, RFM.
    Abstract:
    Synthetic biology constructs often rely upon the introduction of "circuit" genes into host cells, in order to express novel proteins and thus endow the host with a desired behavior. The expression of these new genes "consumes" existing resources in the cell, such as ATP, RNA polymerase, amino acids, and ribosomes. Ribosomal competition among strands of mRNA may be described by a system of nonlinear ODEs called the Ribosomal Flow Model (RFM). The competition for resources between host and circuit genes can be ameliorated by splitting the ribosome pool by use of orthogonal ribosomes, where the circuit genes are exclusively translated by mutated ribosomes. In this work, the RFM system is extended to include orthogonal ribosome competition. This Orthogonal Ribosomal Flow Model (ORFM) is proven to be stable through the use of Robust Lyapunov Functions. The optimization problem of maximizing the weighted protein translation rate by adjusting allocation of ribosomal species is formulated and implemented.


  14. N.Trendel, P. Kruger, S. Gaglione, J. Nguyen, J. Pettmann, E.D. Sontag, and O. Dushek. Perfect adaptation of CD8+ T cell responses to constant antigen input over a wide range of affinity is overcome by costimulation. Science Signaling, 2020. Note: To appear.
    Abstract:
    Maintaining and limiting T cell responses to constant antigen stimulation is critical to control pathogens and maintain self-tolerance, respectively. Antigen recognition by T cell receptors (TCRs) induces signalling that activates T cells to produce cytokines and also leads to the downregulation of surface TCRs. In other systems, receptor downregulation can induce perfect adaptation to constant stimulation by a mechanism known as state-dependent inactivation that requires complete downregulation of the receptor or the ligand. However, this is not the case for the TCR, and therefore, precisely how TCR downregulation maintains or limits T cell responses is controversial. Here, we observed that in vitro expanded primary human T cells exhibit perfect adaptation in cytokine production to constant antigen stimulation across a 100,000-fold variation in affinity with partial TCR downregulation. By directly fitting a mechanistic model to the data, we show that TCR downregulation produces imperfect adaptation, but when coupled to a switch produces perfect adaptation in cytokine production. A pre diction of the model is that pMHC-induced TCR signalling continues after adaptation and this is confirmed by showing that, while costimulation cannot prevent adaptation, CD28 and 4-1BB signalling reactivated adapted T cells to produce cytokines in a pMHC-dependent manner. We show that adaptation also applied to 1st generation chimeric antigen receptor (CAR)-T cells but is partially avoided in 2nd generation CARs. These findings highlight that even partial TCR downregulation can limit T cell responses by producing perfect adaptation rendering T cells dependent on costimulation for sustained responses.


  15. M. Sadeghi, J.M. Greene, and E.D. Sontag. Universal features of epidemic models under social distancing guidelines. bioRxiv, 2020. [WWW] [doi:10.1101/2020.06.21.163931]
    Abstract:
    Different epidemiological models, from the classical SIR system to more sophisticated ones involving population compartments for socially distanced, quarantined, infection aware, asymptomatic infected, and other individuals, share some remarkable dynamic characteristics when contact rates are subject to periodic or one-shot changes. In simple pulsed isolation policies, a linear relationship is found among optimal start time and duration for reduction of the infected peak. If a single interval social distancing starts too early or too late it will be ineffective with respect to decreasing the peak of infection. On the other hand, the nonlinearity of epidemic models leads to non-monotone behavior of the peak of infected population under periodic relaxation policies. This observation led us to hypothesize that an additional single interval social distancing at a proper time can significantly decrease the infected peak of periodic policies, and we verified this improvement.Competing Interest StatementThe authors have declared no competing interest.


  16. A.P. Tran, M. Ali Al-Radhawi, I. Kareva, J. Wu, D.J. Waxman, and E.D. Sontag. Delicate balances in cancer chemotherapy: Modeling immune recruitment and emergence of systemic drug resistance. Frontiers in Immunology, 11:1376-, 2020. [PDF] [doi:10.3389/fimmu.2020.01376] Keyword(s): metronomic chemotherapy, cyclophosphamide, mathematical modeling, immune recruitment, cancer, resistance, oncology, immunology.
    Abstract:
    Metronomic chemotherapy can drastically enhance immunogenic tumor cell death. However, the responsible mechanisms are still incompletely understood. Here, we develop a mathematical model to elucidate the underlying complex interactions between tumor growth, immune system activation, and therapy-mediated immunogenic cell death. Our model is conceptually simple, yet it provides a surprisingly excellent fit to empirical data obtained from a GL261 mouse glioma model treated with cyclophosphamide on a metronomic schedule. The model includes terms representing immune recruitment as well as the emergence of drug resistance during prolonged metronomic treatments. Strikingly, a fixed set of parameters, not adjusted for individuals nor for drug schedule, excellently recapitulates experimental data across various drug regimens, including treatments administered at intervals ranging from 6 to 12 days. Additionally, the model predicts peak immune activation times, rediscovering experimental data that had not been used in parameter fitting or in model construction. The validated model was then used to make predictions about expected tumor-immune dynamics for novel drug administration schedules. Notably, the validated model suggests that immunostimulatory and immunosuppressive intermediates are responsible for the observed phenomena of resistance and immune cell recruitment, and thus for variation of responses with respect to different schedules of drug administration.


  17. A.P. Tran, J.H. Meldon, and E.D. Sontag. Transient diffusion into a bi-layer membrane with mass transfer resistance: Exact solution and time lag analysis. 2020. Note: Submitted.Keyword(s): Bi-layer membrane, transient diffusion, heat conduction, mass transfer resistance.
    Abstract:
    Exact analytical and closed-form solutions to a problem involving transient diffusion in a bi-layer membrane with external transfer resistance are presented. In addition to the solutions of the transient response, the lead and lag times that are often of importance in the characterization of membranes and arise from the analysis of the asymptotic behavior of the mass permeated through the membrane are also provided. The solutions presented here are also compared to previously derived limiting cases of the diffusion in a bi-layer with an impermeable wall and constant concentrations at the upstream and downstream boundaries. Analysis of the time lag shows that this membrane property is independent of the direction of flow. Finally, an outline is provided of how these solutions, which characterize the response to a step function increase in concentration, can be also used to derive more complex input conditions. Adequately handling boundary layer effects has a wide array of potential applications such as the study of bi-layer undergoing phenomena of heat convection, gas film resistance, and absorption/desorption.


  18. A.L. Williams, J.E. Fitzgerald, F. Ivich, E.D. Sontag, and M. Niedre. Short-term circulating tumor cell dynamics in mouse xenograft models and implications for liquid biopsy. 2020. Note: Submitted. Also in bioRxiv 814368; doi: https://doi.org/10.1101/814368. Keyword(s): circulating tumor cells, liquid biopsy, cancer, oncology, multiple myeloma.
    Abstract:
    Circulating tumor cells (CTCs) are widely studied using liquid biopsy methods that analyze single, fractionally-small peripheral blood (PB) samples. However, little is known about fluctuations in CTC numbers that occur over short timescales in vivo, and how these may affect accurate enumeration from blood samples. Diffuse in vivo flow cytometry (DiFC) developed by the Niedre lab allows continuous, non-invasive counting of rare, green fluorescent protein expressing CTCs in large deeply-seated blood vessels in mice. Here, DiFC is used to study short-term changes in CTC numbers in multiple myeloma and Lewis lung carcinoma xenograft models. Both 35- to 50-minute data sets are analyzed, with intervals corresponding to approximately 1, 5, 10 and 20\% of the PB volume, as well as changes over 24-hour periods. For rare CTCs, the use of short DiFC intervals (corresponding to small PB samples) frequently resulted in no detections. For more abundant CTCs, CTC numbers frequently varied by an order of magnitude or more over the time-scales considered. This variability far exceeded that expected by Poisson statistics, and instead was consistent with rapidly changing mean numbers of CTCs in the PB. Because of these natural temporal changes, accurately enumerating CTCs from fractionally small blood samples is inherently problematic. The problem is likely to be compounded for multicellular CTC clusters or specific CTC subtypes. However, it is also shown that enumeration can be improved by averaging multiple samples, analysis of larger volumes, or development of new methods for enumeration of CTCs directly in vivo.



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