From Transcript to Tissue: Multiscale Modeling from Cell Signaling to Matrix Remodeling

[EN] Tissue-level biomechanical properties and function derive from underlying cell signaling, which regulates mass deposition, organization, and removal. Here, we couple two existing modeling frameworks to capture associated multiscale interactions¿one for vessel-level growth and remodeling and one for cell-level signaling¿and illustrate utility by simulating aortic remodeling. At the vessel level, we employ a constrained mixture model describing turnover of individual wall constituents (elastin, intramural cells, and collagen), which has proven useful in predicting diverse adaptations as well as disease progression using phenomenological constitutive relations. Nevertheless, we now seek an improved mechanistic understanding of these processes; we replace phenomenological relations in the mixture model with a logic-based signaling model, which yields a system of ordinary differential equations predicting changes in collagen synthesis, matrix metalloproteinases, and cell proliferation in response to altered intramural stress, wall shear stress, and exogenous angiotensin II. This coupled approach promises improved understanding of the role of cell signaling in achieving tissue homeostasis and allows us to model feedback between vessel mechanics and cell signaling. We verify our model predictions against data from the hypertensive murine infrarenal abdominal aorta as well as results from validated phenomenological models, and consider effects of noisy signaling and heterogeneous cell populations.This work was supported by Grants from the US NIH (R01 HL105297, P01 HL134605, R01 HL139796, U01 HL142518, R01 HL146723)Irons, L.; Latorre, M.; Humphrey, JD. (2021). From Transcript to Tissue: Multiscale Modeling from Cell Signaling to Matrix Remodeling. Annals of Biomedical Engineering. 48(7):1701-1715. https://doi.org/10.1007/s10439-020-02713-81701171548

Modelling cell–matrix interactions in airway smooth muscle cells

Tissues, in both humans and animals, consist of cells embedded in a dynamic scaffold known as the extracellular matrix (ECM). Cells interact with the ECM through the process of cell–matrix adhesion, and these interactions, mediated by transmembrane proteins called integrins, are fundamental in regulating a diverse range of physiological processes. The focus of this thesis is on airway smooth muscle (ASM) cell–matrix adhesion, which regulates the transmission of contractile forces generated within ASM cells to the ECM. This is of particular importance in the context of asthma, where contraction of ASM cells, and the subsequent transmission of contractile forces to the surrounding tissue, leads to a narrowing of the airways called bronchoconstriction. In this thesis, we develop mathematical models of ASM cell–matrix adhesion; our objective is to investigate how integrin-mediated adhesions are affected by the dynamic mechanical environment of the in vivo airway. In particular, we aim to gain insight into how integrins respond to tidal breathing and deep inspirations (DIs), since changes in integrin dynamics may affect the extent of airway narrowing during bronchoconstriction. Firstly, we develop a discrete stochastic–elastic model and a multiscale continuum model (Chapter 2), both able to account for detailed integrin binding kinetics alongside material deformations at the cell level. With these models we observe two distinct adhesion regimes in response to oscillatory loading, where either adhesion formation or adhesion rupture dominate (Chapter 3). For intermediate oscillation amplitudes we observe bistability due to shared loading and, as a result, we find that perturbations in the loading amplitude, mimicking DIs, can lead to different outcomes for the level of adhesion. This will affect the level of attainable force transmission during ASM cell contraction, and we discuss the possible consequences for airway narrowing. There is strong qualitative agreement between our discrete and continuum model results, and we consider several extensions of the continuum model (Chapter 4) to allow for activation, diffusion and strain-dependent reinforcement of integrins. In addition to theoretical results, we present and analyse experimental data from atomic force microscopy experiments (Chapter 5). In the experiments, cells were subject to vertical oscillatory loading of varying amplitudes. By extending the continuum model to support vertical motion, we mimic the experimental protocol and, in agreement with the data, we obtain two distinct temporal patterns in adhesion force. Our simulations provide insight into the underlying integrin dynamics and the resulting cell deformation; these cannot currently be measured by experiments but are predicted by the model. We use cluster analysis techniques to study force timecourses from individual cells and, in some cases, we observe switching behaviours that could be an indicator for bistability. The integrin response to oscillatory loading affects how contractile forces are transmitted from ASM cells to the ECM. However, it is also known that oscillatory loading affects the generation of contractile force (which is mediated by actomyosin crossbridges within the cell). In order to fully understand the consequences for bronchoconstriction, it is therefore important to consider how these processes interact. To investigate this, we couple our model of cell–matrix adhesion to a well-established model of contractile force generation (Chapter 6). Our results demonstrate a close mechanical coupling between the two processes and show that both force transmission (via integrins) and force generation (via crossbridges) are modulated by oscillatory loading. Moreover, there is feedback between the two processes and a regulatory mechanism due to negative feedback. We observe two regions of bistability: one as reported in our earlier results, due to shared loading between integrins, and a second due to analogous mechanisms for the crossbridges. These both introduce hysteresis and can result, in each case, in reduced levels of total contractile force after large amplitude oscillations. It is known from experiments that deep inspirations can induce either transient or sustained bronchodilation, and that these responses differ in asthmatics and non-asthmatics. Because of the hysteresis in total contractile force, we hypothesise that bistability could be an underlying mechanism by which sustained bronchodilation occurs. Furthermore, we show that the bistability can be lost for changes in the passive cell stiffness or in the relative crossbridge to integrin strength; a loss of bistability would result in an inability to obtain sustained reductions in contractile force, which could correspond to the transient bronchodilation seen in asthmatics

The role of mathematical models in designing mechanopharmacological therapies for asthma

Healthy lung function depends on a complex system of interactions which regulate the mechanical and biochemical environment of individual cells to the whole organ. Perturbations from these regulated processes give rise to significant lung dysfunction such as chronic inflammation, airway hyperresponsiveness and airway remodelling characteristic of asthma. Importantly, there is ongoing mechanobiological feedback where mechanical factors including airway stiffness and oscillatory loading have considerable influence over cell behavior. The recently proposed area of mechanophar-macology recognises these interactions and aims to highlight the need to consider mechanobiology when identifying and assessing pharmacological targets. However, these multiscale interactions can be difficult to study experimentally due to the need for measurements across a wide range of spatial and temporal scales. On the other hand, integrative multiscale mathematical models have begun to show success in simulating the interactions between different mechanobiological mechanisms or cell/tissue-types across multiple scales. When appropriately informed by experimental data, these models have the potential to serve as extremely useful predictive tools, where physical mechanisms and emergent behaviours can be probed or hypothesised and, more importantly, exploited to propose new mechanopharmacological therapies for asthma and other respiratory diseases. In this review, we first demonstrate via an exemplar, how a multiscale mathematical model of acute bron-choconstriction in an airway could be exploited to propose new mechanopharmacological therapies. We then review current mathematical modelling approaches in respiratory disease and highlight hypotheses generated by such models that could have significant implications for therapies in asthma, but that have not yet been the subject of experimental attention or investigation. Finally we highlight modelling approaches that have shown promise in other biological systems that could be brought to bear in developing mathematical models for optimisation of mechanopharmacolog-ical therapies in asthma, with discussion of how they could complement and accelerate current experimental approaches

Microstructural influences on growth and transport in biological tissue—a multiscale description

The detailed understanding of growth and transport dynamics within biological tissue is made particularly challenging by the complex and multiscale nature of this medium. For this reason so-called effective descriptions are frequently sought. These offer coarse-scale models that still accommodate aspects of microscale dynamics. When considering tissue growth, such formulations must accommodate the continuous growth and remodeling processes that occur in response to environmental cues. As a model system for investigating relevant phenomena, in this chapter we consider nutrient-limited growth of a porous medium (with broad application to vascularized tumor growth). Using asymptotic homogenization we derive the macroscale equations that describe a ‘double porous medium’ whose flow is influenced by both the tissue microstructure and growth that occurs in response to nutrient transport governed by an advection–reaction equation. The coupled flow and transport dynamics are demonstrated by numerical experiments indicating the influence of microscale structure and transport phenomena on the macroscale dynamics. The importance of slip, tortuosity, and of nutrient-limited growth are considered

Effect of loading history on airway smooth muscle cell-matrix adhesions

Integrin-mediated adhesions between airway smooth muscle (ASM) cells and the extracellular matrix (ECM) regulate how contractile forces generated within the cell are transmitted to its external environment. Environmental cues are known to influence the formation, size and survival of cell-matrix adhesions, but it is not yet known how they are affected by dynamic fluctuations associated with tidal breathing in the intact airway. Here we develop two closely-related theoretical models to study adhesion dynamics in response to oscillatory loading of the ECM, representing the dynamic environment of ASM cells in vivo. Using a discrete stochastic-elastic model, we simulate individual integrin binding and rupture events and observe two stable regimes in which either bond formation or bond rupture dominate, depending on the amplitude of the oscillatory loading. These regimes have either a high or low fraction of persistent adhesions, which could affect the level of strain transmission between contracted ASM cells and the airway tissue. For intermediate loading we observe a region of bistability and hysteresis due to shared loading between existing bonds; the level of adhesion depends on the loading history. These findings are replicated in a related continuum model, which we use to investigate the effect of perturbations mimicking deep inspirations (DIs). Due to the bistability, a DI applied to the high adhesion state could either induce a permanent switch to a lower adhesion state or allow a return of the system to the high adhesion state. Transitions between states are further influenced by the frequency of oscillations, cytoskeletal or ECM stiffnesses and binding affinities, which modify the magnitudes of the stable adhesion states as well as the region of bistability. These findings could explain (in part) the transient bronchodilatory effect of a DI observed in asthmatics compared to a more sustained effect in normal subjects

Switching behaviour in vascular smooth muscle cell–matrix adhesion during oscillatory loading

Integrins regulate mechanotransduction between smooth muscle cells (SMCs) and the extracellular matrix (ECM). SMCs resident in the walls of airways or blood vessels are continuously exposed to dynamic mechanical forces due to breathing or pulsatile blood flow. However, the resulting effects of these forces on integrin dynamics and associated cell-matrix adhesion are not well understood. Here we present experimental results from atomic force microscopy (AFM) experiments, designed to study the integrin response to external oscillatory loading of varying amplitudes applied to live aortic SMCs, together with theoretical results from a mathematical model. In the AFM experiments, a fibronectin-coated probe was used cyclically to indent and retract from the surface of the cell. We observed a transition between states of firm adhesion and of complete detachment as the amplitude of oscillatory loading increased, revealed by qualitative changes in the force timecourses. Interestingly, for some of the SMCs in the experiments, switching behaviour between the two adhesion states is observed during single timecourses at intermediate amplitudes. We obtain two qualitatively similar adhesion states in the mathematical model, where we simulate the cell, integrins and ECM as an evolving system of springs, incorporating local integrin binding dynamics. In the mathematical model, we observe a region of bistability where both the firm adhesion and detachment states can occur depending on the initial adhesion state. The differences are seen to be a result of mechanical cooperativity of integrins and cell deformation. Switching behaviour is a phenomenon associated with bistability in a stochastic system, and bistability in our deter-ministic mathematical model provides a potential physical explanation for the experimental results. Physiologically, bistability provides a means for transient mechanical stimuli to induce long-term changes in adhesion dynamics-and thereby the cells' ability to transmit force-and we propose further experiments for testing this hypothesis

In cultured cells the baculovirus P10 protein forms two independent intracellular structures that play separate roles in occlusion body maturation and their release by nuclear disintegration

P10 is a small, abundant baculovirus protein that accumulates to high levels in the very late stages of the infection cycle. It is associated with a number of intracellular structures and implicated in diverse processes from occlusion body maturation to nuclear stability and lysis. However, studies have also shown that it is non-essential for virus replication, at least in cell culture. Here, we describe the use of serial block-face scanning electron microscopy to achieve high-resolution 3D characterisation of P10 structures within Trichoplusia ni TN-368 cells infected with Autographa californica multiple nucleopolyhedrovirus. This has enabled unparalleled visualisation of P10 and determined the independent formation of dynamic perinuclear and nuclear vermiform fibrous structures. Our 3D data confirm the sequence of ultrastructural changes that create a perinuclear cage from thin angular fibrils within the cytoplasm. Over the course of infection in cultured cells, the cage remodels to form a large polarised P10 mass and we suggest that these changes are critical for nuclear lysis to release occlusion bodies. In contrast, nuclear P10 forms a discrete vermiform structure that was observed in close spatial association with both electron dense spacers and occlusion bodies; supporting a previously suggested role for P10 and electron dense spacers in the maturation of occlusion bodies. We also demonstrate that P10 hyper-expression is critical for function. Decreasing levels of p10 expression, achieved by manipulation of promoter length, correlated with reduced P10 production, a lack of formation of P10 structures and a concomitant decrease in nuclear lysis

The Genetic Signature of Sex-Biased Migration in Patrilocal Chimpanzees and Humans

A large body of theoretical work suggests that analyses of variation at the maternally inherited mitochondrial (mt)DNA and the paternally inherited non-recombining portion of the Y chromosome (NRY) are a potentially powerful way to reveal the differing migratory histories of men and women across human societies. However, the few empirical studies comparing mtDNA and NRY variation and known patterns of sex-biased migration have produced conflicting results. Here we review some methodological reasons for these inconsistencies, and take them into account to provide an unbiased characterization of mtDNA and NRY variation in chimpanzees, one of the few mammalian taxa where males routinely remain in and females typically disperse from their natal groups. We show that patterns of mtDNA and NRY variation are more strongly contrasting in patrilocal chimpanzees compared with patrilocal human societies. The chimpanzee data we present here thus provide a valuable comparative benchmark of the patterns of mtDNA and NRY variation to be expected in a society with extremely female-biased dispersal

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology