Diffusion anisotropy in collagen gels and tumors: the effect of fiber network orientation

Modeling collagen fibril degradation as a function of matrix microarchitecture

Collagenolytic degradation is a process fundamental to tissue remodeling. The microarchitecture of collagen fibril networks changes during development, aging, and disease. Such changes to microarchitecture are often accompanied by changes in matrix degradability. In vitro, collagen matrices of the same concentration but different microarchitectures also vary in degradation rate. How do different microarchitectures affect matrix degradation? To answer this question, we developed a computational model of collagen degradation. We first developed a lattice model that describes collagen degradation at the scale of a single fibril. We then extended this model to investigate the role of microarchitecture using Brownian dynamics simulation of enzymes in a multi-fibril three dimensional matrix to predict its degradability. Our simulations predict that the distribution of enzymes around the fibrils is non-uniform and depends on the microarchitecture of the matrix. This non-uniformity in enzyme distribution can lead to different extents of degradability for matrices of different microarchitectures. Our model predictions were tested using in vitro experiments with synthesized collagen gels of different microarchitectures. Experiments showed that indeed degradation of collagen depends on the matrix architecture and fibril thickness. In summary, our study shows that the microarchitecture of the collagen matrix is an important determinant of its degradability.

Particle dispersion through porous media with heterogeneous attractions

Porous media used in many practical applications contain natural spatial variations in composition and surface charge that lead to heterogeneous physicochemical attractions between the media and transported particles. We performed Stokesian dynamics (SD) simulations to examine the effects of heterogeneous attractions on quiescent diffusion and hydrodynamic dispersion of particles within geometrically ordered arrays of nanoposts. We find that transport under quiescent conditions occurs by two mechanisms, diffusion through the void space and intermittent hopping between the attractive wells of different nanoposts. As the attraction heterogeneity increases, the latter mechanism becomes dominant, resulting in an increase in the particle trajectory tortuosity, deviations from Gaussian behavior in the particle displacement distributions, and a decrease in the long-time particle diffusivity. Similarly, under flow conditions corresponding to low Péclet number (Pe), increased attraction heterogeneity leads to transient localization near the nanoposts, resulting in a broadening of the particle distribution and enhanced longitudinal dispersion in the direction of flow. At high Pe where advection strongly dominates, however, the longitudinal dispersion coefficient is insensitive to attraction heterogeneity and exhibits Taylor-Aris dispersion behavior. Our findings provide insight into how heterogeneous interactions may influence particle transport in complex 3-D porous media.

Expanding the applicability of multiphoton fluorescence recovery after photobleaching by incorporating shear stress in laminar flow

Significance

Multi-photon fluorescence recovery after photobleaching (MPFRAP) is a nonlinear microscopy technique used to measure the diffusion coefficient of fluorescently tagged molecules in solution. Previous MPFRAP fitting models calculate the diffusion coefficient in systems with diffusion or diffusion in laminar flow.

Aim

We propose an MPFRAP fitting model that accounts for shear stress in laminar flow, making it a more applicable technique for in vitro and in vivo studies involving diffusion.

Approach

Fluorescence recovery curves are generated using high-throughput molecular dynamics simulations and then fit to all three models (diffusion, diffusion and flow, and diffusion and shear flow) to define the limits within which accurate diffusion coefficients are produced. Diffusion is simulated as a random walk with a variable horizontal bias to account for shear flow.

Results

Contour maps of the accuracy of the fitted diffusion coefficient as a function of scaled velocity and scaled shear rate show the parameter space within which each model produces accurate diffusion coefficients; the shear-flow model covers a larger area than the previous models.

Conclusion

The shear-flow model allows MPFRAP to be a viable optical tool for studying more biophysical systems than previous models.

Anomalous diffusion of nanoparticles in the spatially heterogeneous biofilm environment

Biofilms contain extracellular polymeric substances (EPS) that provide structural support and restrict penetration of antimicrobial treatment. To overcome limited penetration, functionalized nanoparticles (NPs) have been suggested as carriers for antimicrobial delivery. Using microscopy, we evaluate the diffusion of nanoparticles in function of the structure of Salmonella biofilms. We observe anomalous diffusion and heterogeneous mobility of NPs resulting in distinct NPs distribution that depended on biofilm structure. Through Brownian dynamics modeling with spatially varying viscosity around bacteria, we demonstrated that spatial gradients in diffusivity generate viscous sinks that trap NPs near bacteria. This model replicates the characteristic diffusion signature and vertical distribution of NPs in the biofilm. From a treatment perspective, our work indicates that both biofilm structure and the level of EPS can impact NP drug delivery, where low levels of EPS might benefit delivery by immobilizing NPs closer to bacteria and higher levels hamper delivery due to shielding effects.

Precision Hydrogels for the Study of Cancer Cell Mechanobiology

Cancer progression is associated with extensive remodeling of the tumor microenvironment (TME), resulting in alterations of biochemical and biophysical cues that affect both cancer and stromal cells. In particular, the mechanical characteristics of the TME extracellular matrix undergo significant changes. Bioengineered polymer hydrogels can be instrumental to systematically explore how mechanically changed microenvironments impact cancer cell behavior, including proliferation, survival, drug resistance, and invasion. This article reviews studies that have explored the impact of different mechanical cues of the cells' 3D microenvironment on cancer cell behavior using hydrogel-based in vitro models. In particular, advanced engineering strategies are highlighted for tailored hydrogel matrices recapitulating the TME's micrometer- and sub-micrometer-scale architectural and mechanical features, while accounting for its intrinsically heterogenic and dynamic nature. It is anticipated that such precision hydrogel systems will further the understanding of cancer mechanobiology.

Radiotherapy-induced tumor physical microenvironment remodeling to overcome immunotherapy resistance

The clinical benefits of immunotherapy are proven in many cancers, but a significant number of patients do not respond well to immunotherapy. The tumor physical microenvironment (TpME) has recently been shown to affect the growth, metastasis and treatment of solid tumors. The tumor microenvironment (TME) has unique physical hallmarks: 1) unique tissue microarchitecture, 2) increased stiffness, 3) elevated solid stress, and 4) elevated interstitial fluid pressure (IFP), which contribute to tumor progression and immunotherapy resistance in a variety of ways. Radiotherapy, a traditional and powerful treatment, can remodel the matrix and blood flow associated with the tumor to improve the response rate of immune checkpoint inhibitors (ICIs) to a certain extent. Herein, we first review the recent research advances on the physical properties of the TME and then explain how TpME is involved in immunotherapy resistance. Finally, we discuss how radiotherapy can remodel TpME to overcome immunotherapy resistance.

Molecular Simulation of Hopping Mechanisms of Nanoparticles in Regular Cross-Linked Polymer Networks

We use coarse-grained simulations to explore the diffusion mechanism of nanoparticles with different sizes at various nanoparticle-polymer interactions in regular cross-linked polymer networks. The long time diffusivities of nanoparticles show a non-monotonic tendency at various nanoparticle-polymer interactions, due to the intermittent hopping of nanoparticles through network cells. The preferred locations of small nanoparticles switch from the cell centers to the corner of cells as they interact with network more strongly, which results in the hopping energy barrier between different cells switching from cell center localization to adsorption on networks. Steric hindrance seriously hampers large nanoparticles from hopping to neighboring network cells, the interactions between nanoparticle and network enhance the network deformability and also affect the hopping of nanoparticles. The multiple constraint mechanisms result in the non-monotonic diffusivities of nanoparticles with different interactions and non-Brownian motions at different time scales. Our work illustrates the hopping mechanisms of nanoparticles in polymer networks from thermodynamic and dynamic points of view.

Molecular and Colloidal Transport in Bacterial Cellulose Hydrogels

Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. The design of diverse applications of these bacterial cellulose films also relies on understanding and controlling transport through the fiber mesh, and transport simulations of the films are most accurate when guided by experimental characterization of the structures and the resultant diffusion inside. Diffusion through such films is a function of their key microstructural length scales, determining how molecules, as well as particles and microorganisms, permeate them. We use microscopy to study the unique bacterial cellulose film via its pore structure and quantify the mobility dynamics of various sizes of tracer particles and macromolecules. Mobility is hindered within the films, as confinement and local movement strongly depend on the void size relative to diffusing tracers. The biofilms have a naturally periodic structure of alternating dense and porous layers of nanofiber mesh, and we tune the magnitude of the spacing via fermentation conditions. Micron-sized particles can diffuse through the porous layers but cannot penetrate the dense layers. Tracer mobility in the porous layers is isotropic, indicating a largely random pore structure there. Molecular diffusion through the whole film is only slightly reduced by the structural tortuosity. Knowledge of transport variations within bacterial cellulose networks can be used to guide the design of symbiotic cultures in these structures and enhance their use in applications like biomedical implants, wound dressings, lab-grown meat, clothing textiles, and sensors.

Nanoparticle dispersion in porous media: Effects of attractive particle-media interactions

We investigate the effects of physicochemical attractions on the transport of finite-sized particles in three-dimensional ordered nanopost arrays using Stokesian dynamics simulations. We find that weak particle-nanopost attractions negligibly affect diffusion due to the dominance of Brownian fluctuations. Strong attractions, however, significantly hinder particle diffusion due to localization of particles around the nanoposts. Conversely, under flow, attractions significantly enhance longitudinal dispersion at low to moderate Péclet number (Pe). At high Pe, by contrast, advection becomes dominant and attractions weakly enhance dispersion. Moreover, attractions frustrate directional locking at moderate flow rates, and shift the onset of this behavior to higher Pe.

Elucidating the signal for contact guidance contained in aligned fibrils with a microstructural-mechanical model

Despite its importance in physiological processes and tissue engineering, the mechanism underlying cell contact guidance in an aligned fibrillar network has defied elucidation due to multiple interdependent signals that such a network presents to cells, namely, anisotropy of adhesion, porosity and mechanical behaviour. A microstructural-mechanical model of fibril networks was used to assess the relative magnitudes of these competing signals in networks of varied alignment strength based on idealized cylindrical pseudopods projected into the aligned and orthogonal directions and computing the anisotropy of metrics chosen for adhesion, porosity and mechanical behaviour: cylinder-fibre contact area for adhesion, persistence length of pores for porosity and total force to displace fibres from the cylindrical volume as well as network stiffness experienced upon cylinder retraction for mechanical behaviour. The signals related to mechanical anisotropy are substantially higher than adhesion and porosity anisotropy, especially at stronger network alignments, although their signal to noise (S/N) values are substantially lower. The former finding is consistent with a recent report that fibroblasts can sense fibril alignment via anisotropy of network mechanical resistance, and the model reveals this can be due to either mechanical resistance to pseudopod protrusion or retraction given their signal and S/N values are similar.

Revisiting the role of pulsed electric fields in overcoming the barriers to in vivo gene electrotransfer

Gene therapies are revolutionizing medicine by providing a way to cure hitherto incurable diseases. The scientific and technological advances have enabled the first gene therapies to become clinically approved. In addition, with the ongoing COVID-19 pandemic, we are witnessing record speeds in the development and distribution of gene-based vaccines. For gene therapy to take effect, the therapeutic nucleic acids (RNA or DNA) need to overcome several barriers before they can execute their function of producing a protein or silencing a defective or overexpressing gene. This includes the barriers of the interstitium, the cell membrane, the cytoplasmic barriers and (in case of DNA) the nuclear envelope. Gene electrotransfer (GET), i.e., transfection by means of pulsed electric fields, is a non-viral technique that can overcome these barriers in a safe and effective manner. GET has reached the clinical stage of investigations where it is currently being evaluated for its therapeutic benefits across a wide variety of indications. In this review, we formalize our current understanding of GET from a biophysical perspective and critically discuss the mechanisms by which electric field can aid in overcoming the barriers. We also identify the gaps in knowledge that are hindering optimization of GET in vivo.

Modeling Innate Antiviral Immunity in Physiological Context

An effective innate antiviral response is critical for the mitigation of severe disease and host survival following infection. In vivo, the innate antiviral response is triggered by cells that detect the invading pathogen and then communicate through autocrine and paracrine signaling to stimulate the expression of genes that inhibit viral replication, curtail cell proliferation, or modulate the immune response. In other words, the innate antiviral response is complex and dynamic. Notably, in the laboratory, culturing viruses and assaying viral life cycles frequently utilizes cells that are derived from tissues other than those that support viral replication during natural infection, while the study of viral pathogenesis often employs animal models. In recapitulating the human antiviral response, it is important to consider that variation in the expression and function of innate immune sensors and antiviral effectors exists across species, cell types, and cell differentiation states, as well as when cells are placed in different contexts. Thus, to gain novel insight into the dynamics of the host response and how specific sensors and effectors impact infection kinetics by a particular virus, the model system must be selected carefully. In this review, we briefly introduce key signaling pathways involved in the innate antiviral response and highlight how these differ between systems. We then review the application of tissue-engineered or 3D models for studying the antiviral response, and suggest how these in vitro culture systems could be further utilized to assay physiologically-relevant host responses and reveal novel insight into virus-host interactions.

Effect of ALDH1A1 Gene Knockout on Drug Resistance in Paclitaxel and Topotecan Resistant Human Ovarian Cancer Cell Lines in 2D and 3D Model

Ovarian cancer is the most common cause of gynecological cancer death. Cancer Stem Cells (CSCs) characterized by drug transporters and extracellular matrix (ECM) molecules expression are responsible for drug resistance development. The goal of our study was to examine the role of aldehyde dehydrogenase 1A1 (ALDH1A1) expression in paclitaxel (PAC) and topotecan (TOP) resistant ovarian cancer cell lines. In both cell lines, we knocked out the ALDH1A1 gene using the CRISPR/Cas9 technique. Additionally, we derived an ALDH1A1 positive TOP-resistant cell line with ALDH1A1 expression in all cells via clonal selection. The effect of ALDH1A1 gene knockout or clonal selection on the expression of ALDH1A1, drug transporters (P-gp and BCRP), and ECM (COL3A1) was determined by Q-PCR, Western blot and immunofluorescence. Using MTT assay, we compared drug resistance in two-dimensional (2D) and three-dimensional (3D) cell culture conditions. We did not observe any effect of ALDH1A1 gene knockout on MDR1/P-gp expression and drug resistance in the PAC-resistant cell line. The knockout of ALDH1A1 in the TOP-resistant cell line resulted in a moderate decrease of BCRP and COL3A1 expression and weakened TOP resistance. The clonal selection of ALDH1A1 cells resulted in very strong downregulation of BCPR and COL3A1 expression and overexpression of MDR1/P-gp. This finally resulted in decreased resistance to TOP but increased resistance to PAC. All spheroids were more resistant than cells growing as monolayers, but the resistance mechanism differs. The spheroids' resistance may result from the presence of cell zones with different proliferation paces, the density of the spheroid, ECM expression, and drug capacity to diffuse into the spheroid.

Hydrodynamics induce superdiffusive jumps of passive tracers along critical paths of random networks and colloidal gels

We present a numerical study on the effect of hydrodynamic interactions (HI) on the diffusion of inert point tracer particles in several fixed random structures. As expected, the diffusion is hampered by the extra hydrodynamic friction introduced by the obstacle network. However, a non-trivial effect due to HI appears in the analysis of the van-Hove displacement probability close to the percolation threshold, where tracers diffuse through critical fractal paths. We show that the tracer dynamics can be split up into short and long jumps, the latter being ruled by either exponential or Gaussian van Hove distribution tails. While at short time HI slow down the tracer diffusion, at long times, hydrodynamic interactions with the obstacles increase the probability of longer jumps, which circumvent the traps of the labyrinth more easily. Notably, the relation between the anomalous diffusion exponent and the fractal dimension of the critical (intricate) paths is greater than one, which implies that the long-time (long-jump) diffusion is mildly superdiffuse. A possible reason for such a hastening of the diffusion along the network corridors is the hydrodynamically induced mobility anisotropy, which favours displacements parallel to the walls, an effect which has already been experimentally observed in collagen gels.

A Nonparametric Approach for Estimating Three-Dimensional Fiber Orientation Distribution Functions (ODFs) in Fibrous Materials

Many biological tissues contain an underlying fibrous microstructure that is optimized to suit a physiological function. The fiber architecture dictates physical characteristics such as stiffness, diffusivity, and electrical conduction. Abnormal deviations of fiber architecture are often associated with disease. Thus, it is useful to characterize fiber network organization from image data in order to better understand pathological mechanisms. We devised a method to quantify distributions of fiber orientations based on the Fourier transform and the Qball algorithm from diffusion MRI. The Fourier transform was used to decompose images into directional components, while the Qball algorithm efficiently converted the directional data from the frequency domain to the orientation domain. The representation in the orientation domain does not require any particular functional representation, and thus the method is nonparametric. The algorithm was verified to demonstrate its reliability and used on datasets from microscopy to show its applicability. This method increases the ability to extract information of microstructural fiber organization from experimental data that will enhance our understanding of structure-function relationships and enable accurate representation of material anisotropy in biological tissues.

Towards principled design of cancer nanomedicine to accelerate clinical translation

Nanotechnology in medical applications, especially in oncology as drug delivery systems, has recently shown promising results. However, although these advances have been promising in the pre-clinical stages, the clinical translation of this technology is challenging. To create drug delivery systems with increased treatment efficacy for clinical translation, the physicochemical characteristics of nanoparticles such as size, shape, elasticity (flexibility/rigidity), surface chemistry, and surface charge can be specified to optimize efficiency for a given application. Consequently, interdisciplinary researchers have focused on producing biocompatible materials, production technologies, or new formulations for efficient loading, and high stability. The effects of design parameters can be studied in vitro, in vivo, or using computational models, with the goal of understanding how they affect nanoparticle biophysics and their interactions with cells. The present review summarizes the advances and technologies in the production and design of cancer nanomedicines to achieve clinical translation and commercialization. We also highlight existing challenges and opportunities in the field.

Histogram analysis based on diffusion kurtosis imaging: Differentiating glioblastoma multiforme from single brain metastasis and comparing the diagnostic performance of two region of interest placements

PURPOSE

To assess the value of histogram analysis, using diffusion kurtosis imaging (DKI), in differentiating glioblastoma multiforme (GBM) from single brain metastasis (SBM) and to compare the diagnostic efficiency of different region of interest (ROI) placements.

METHOD

Sixty-seven patients with histologically confirmed GBM (n = 35) and SBM (n = 32) were recruited. Two ROIs-the contrast-enhanced area and whole-tumor area-were delineated across all slices. Eleven histogram parameters of fractional anisotropy (FA), mean diffusivity (MD), and mean kurtosis (MK) from both ROIs were calculated. All histogram parameter values were compared between GBM and SBM, using the Mann-Whitney U test. The accuracies of different histogram parameters were compared using the McNemar test. Receiver operating characteristic (ROC) analyses were conducted to assess the diagnostic performance.

RESULTS

In the contrast-enhanced area, FA₁₀, FA₂₅, FA₇₅, FA₉₀, FA_mean, FA_median, FA_max, MD_max, MD_skewness, and MK_skewness were significantly higher for GBM than for SBM. FA_skewness was significantly lower for GBM than for SBM. FA₂₅ (0.815) had the highest area under the curve (AUC). In the whole-tumor area, FA₁₀, FA₂₅, FA₇₅, FA₉₀, FA_SD, FA_mean, FA_median, FA_max, MD_max, MD_skewness, and MK_skewness were significantly higher for GBM than for SBM. FA_median (0.805) had the highest AUC. The accuracy of FA₂₅ in the contrast-enhanced area was significantly higher than that of the FA_median in the whole-tumor area.

CONCLUSIONS

GBM and SBM can be differentiated using the DKI-based histogram analysis. Placing the ROI on the contrast-enhanced area results in better discrimination.

Relationship of shear wave elastography anisotropy with tumor stem cells and epithelial-mesenchymal transition in breast cancer

Background

This study is to examine the feasibility of shear wave elastography (SWE) anisotropy in assessing the prognosis of breast cancer.

Methods

We enrolled 119 breast cancer patients from January 2017 to October 2019. SWE was performed before operation. Emax (maximum elasticity value), Emean (average elasticity value), Esd (standard deviation of the lesion elasticity value), Eratio (elasticity value of adipose tissue), anisotropy coefficient and difference were recorded. After operation, we collected clinical pathological data, and performed immunohistochemistry and real-time PCR tests on CD44, CD24, E-cadherin, β-catenin, vimentin and N-cadherin. Finally, we analyzed the correlation among parameters of SWE, anisotropy and clinicopathology, and markers of CSCs (cancer stem cells) and EMT (epithelial-mesenchymal transition).

Results

Emax, Emean and Esd of the cross section were higher than those of the longitudinal section. Breast cancer with a higher elastic modulus was often accompanied by a hyperechoic halo, which was manifested as mixed echo and post-echo attenuation, and was accompanied by a higher BI-RADS (breast imaging reporting and data system) classification. When breast cancer had hyperechoic halo and weakened posterior echo, SWE of the lesion showed more obvious anisotropy. In addition, larger diameter of the longitudinal section indicated higher stiffness of the cross section. Correlation analysis showed that E-cadherin was negatively correlated with SWE in longitudinal section. CD44, N-cadherin, β-catenin were positively correlated with SWE in longitudinal and cross sections. Vimentin and CD24 had no correlation with SWE parameters.

Conclusion

SWE of breast cancer is anisotropic. The cross-sectional SWE is better than the longitudinal SWE, Emax is better than Emean, the anisotropy of SWE is better than SWE, and the anisotropy factor is better than the anisotropy difference.

The Effect of the Layered Internal Structure of Fibrous Beds on the Hydrodynamic Diffusive Behavior of Microparticles

To separate and collect microparticles such as cells, the behavior of particles in fibrous filters was investigated. It is essential to understand, in detail, the motion of particles in microscale flows, because Re is often small, and particles exhibit complex behaviors such as changes in relative position and spreading owing to hydrodynamic interactions. We calculated the motion of microparticles passing through the fibrous bed using the Stokesian dynamics method, in which hydrodynamic interaction is considered, theoretically. The fibrous bed was modeled by particles and five types of structures (a monolayer with fiber volume fractions φ of 3%, 4%, and 5%, and a bilayer with φ = 3%−5% and 5%−3%) were considered. Our numerical results showed that the particles moved in a complicated manner, and spread throughout the fibrous bed. It was found that the behavior of individual microparticles varied depending on the internal structure, although the average permeation velocity was primarily determined by the fiber volume fraction. This great dependence of the behavior of particle assemblage on the internal structure of the fibrous bed was caused by the individual particle motion under the influence of the layers in front of and behind them, owing to the hydrodynamic interaction.

Nanoparticle dispersion in porous media: Effects of array geometry and flow orientation

We investigate the effects of array geometry and flow orientation on transport of finite-sized particles in ordered arrays using Stokesian dynamics simulations. We find that quiescent diffusion is independent of array geometry over the range of volume fraction of the nanoposts examined. Longitudinal dispersion under flow depends on the direction of incident flow relative to the array lattice vectors. Taylor-Aris behavior is recovered for flow along the lattice directions, whereas a nonmonotonic dependence of the dispersion coefficient on the Péclet number is obtained for flow orientations slightly perturbed from certain lattice vectors, owing to a competition between directional locking and spatial velocity variations.

Evaluating parameters affecting drug fate at the intramuscular injection site

Intramuscular (IM) injections are a well-established method of delivering a variety of therapeutics formulated for parenteral administration. While the wide range of commercial IM pharmaceuticals provide a wealth of pharmacokinetic (PK) information following injection, there remains an inadequate understanding of drug fate at the IM injection site that could dictate these PK outcomes. An improved understanding of injection site events could improve approaches taken by formulation scientists to identify therapeutically effective and consistent drug PK outcomes. Interplay between the typically non-physiological aspects of drug formulations and the homeostatic IM environment may provide insights into the fate of drugs at the IM injection site, leading to predictions of how a drug will behave post-injection in vivo. Immune responses occur by design after e.g. vaccine administration, however immune responses post-injection are not in the scope of this article. Taking cues from existing in vitro modelling technologies, the purpose of this article is to propose "critical parameters" of the IM environment that could be examined in hypothesis-driven studies. Outcomes of such studies might ultimately be useful in predicting and improving in vivo PK performance of IM injected drugs.

3D random walk model of diffusion in human Hypo- and Hyper- mineralized collagen fibrils

Bone tissue is composed at the nanoscale of apatite minerals, collagen molecules and water that form the mineralized collagen fibril (MCF). Water has a crucial role in bone biomineralization. We developed a 3D random walk model to investigate the water diffusion process within the MCF for three different scenarios, namely low, intermediate and high mineral volume fraction. The MCF geometric model is obtained after applying 6·10⁶ translational and rotational perturbations to an ordered arrangement of mineral. Subsequently, we compute 300 random trajectories of water molecules within the MCF for each mineral volume fraction. Every trajectory is constituted of up to 500 k positions of the water particle. We determined the diffusion coefficient from the linear fit of the mean squared displacement of water molecules as a function of time. We investigate changes in the diffusivity values in relation to variation of bone mineral content. The analysis performed on the random walk data, for all mineralization conditions, leads to diffusion coefficients in good agreement with the diffusivity outcomes achieved from previous experimental studies. Thus, the 3D geometrical configuration adopted in this numerical study appears suitable for modelling the MCF with different volume fractions, from hypo- to hyper-mineralized conditions. We observed that low mineral content is associated with an increase of the water diffusion, while lower values of diffusivity are determined in hypermineralized conditions. In agreement with experimental data, our results highlight the influence of the structural alterations on the mass transport properties.

A novel modelling and simulation approach for the hindered mobility of charged particles in biological hydrogels

This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random three-dimensional fibre orientation and connectivity of the biopolymer network and that accounts for elastic deformations of the fibres by means of beam theory. As a key component of the model, novel formulations are proposed both for the electrostatic and repulsive steric interactions between a spherical particle and a beam. In addition to providing a thorough validation of the model, the presented computational studies yield new insights into the underlying mechanisms of hindered particle mobility, especially regarding the influence of the aforementioned aspects that are unique to this model. It is found that the precise distribution of fibre and thus charge agglomerations in the network have a crucial influence on the mobility of oppositely charged particles and gives rise to distinct motion patterns. Considering the high practical significance for instance with respect to targeted drug release or infection defence, the provided proof of concept motivates further advances of the model towards a truly predictive computational tool that allows a case- and patient-specific assessment for real (biological) systems.

Piperine Targets Different Drug Resistance Mechanisms in Human Ovarian Cancer Cell Lines Leading to Increased Sensitivity to Cytotoxic Drugs

Our goal was to examine the anticancer effects of piperine against the resistant human ovarian cancer cells and to explore the molecular mechanisms responsible for its anticancer effects. Our study used drug-sensitive ovarian cancer cell line W1 and its sublines resistant to paclitaxel (PAC) and topotecan (TOP). We analyzed the cytotoxic effect of piperine and cytostatic drugs using an MTT assay. The impact of piperine on protein expression was determined by immunofluorescence and Western blot. We also examined its effect on cell proliferation and migration. We noticed a different level of piperine resistance between cell lines. Piperine increases the cytotoxic effect of PAC and TOP in drug-resistant cells. We observed an increase in PTPRK expression correlated with decreased pTYR level after piperine treatment and downregulation of P-gp and BCRP expression. We also noted a decrease in COL3A1 and TGFBI expression in investigated cell lines and increased COL3A1 expression in media from W1PR2 cells. The expression of Ki67 protein and cell proliferation rate decreased after piperine treatment. Piperine markedly inhibited W1TR cell migration. Piperine can be considered a potential anticancer agent that can increase chemotherapy effectiveness in cancer patients.

Measuring Nanoparticle Penetration Through Bio-Mimetic Gels

Background

In cancer nanomedicine, drugs are transported by nanocarriers through a biological system to produce a therapeutic effect. The efficacy of the treatment is affected by the ability of the nanocarriers to overcome biological transport barriers to reach their target. In this work, we focus on the process of nanocarrier penetration through tumour tissue after extravasation. Visualising the dynamics of nanocarriers in tissue is difficult in vivo, and in vitro assays often do not capture the spatial and physical constraints relevant to model tissue penetration.

Methods

We propose a new simple, low-cost method to observe the transport dynamics of nanoparticles through a tissue-mimetic microfluidic chip. After loading a chip with triplicate conditions of gel type and loading with microparticles, microscopic analysis allows for tracking of fluorescent nanoparticles as they move through hydrogels (Matrigel and Collagen I) with and without cell-sized microparticles. A bespoke image-processing codebase written in MATLAB allows for statistical analysis of this tracking, and time-dependent dynamics can be determined.

Results

To demonstrate the method, we show size-dependence of transport mechanics can be observed, with diffusion of fluorescein dye throughout the channel in 8 h, while 20 nm carboxylate FluoSphere diffusion was hindered through both Collagen I and Matrigel™. Statistical measurements of the results are generated through the software package and show the significance of both size and presence of microparticles on penetration depth.

Conclusion

This provides an easy-to-understand output for the end user to measure nanoparticle tissue penetration, enabling the first steps towards future automated experimentation of transport dynamics for rational nanocarrier design.

A noninvasive fluorescence imaging-based platform measures 3D anisotropic extracellular diffusion

Diffusion is a major molecular transport mechanism in biological systems. Quantifying direction-dependent (i.e., anisotropic) diffusion is vitally important to depicting how the three-dimensional (3D) tissue structure and composition affect the biochemical environment, and thus define tissue functions. However, a tool for noninvasively measuring the 3D anisotropic extracellular diffusion of biorelevant molecules is not yet available. Here, we present light-sheet imaging-based Fourier transform fluorescence recovery after photobleaching (LiFT-FRAP), which noninvasively determines 3D diffusion tensors of various biomolecules with diffusivities up to 51 µm2 s-1, reaching the physiological diffusivity range in most biological systems. Using cornea as an example, LiFT-FRAP reveals fundamental limitations of current invasive two-dimensional diffusion measurements, which have drawn controversial conclusions on extracellular diffusion in healthy and clinically treated tissues. Moreover, LiFT-FRAP demonstrates that tissue structural or compositional changes caused by diseases or scaffold fabrication yield direction-dependent diffusion changes. These results demonstrate LiFT-FRAP as a powerful platform technology for studying disease mechanisms, advancing clinical outcomes, and improving tissue engineering.

Bioactivity Comparison of Electrospun PCL Mats and Liver Extracellular Matrix as Scaffolds for HepG2 Cells

Cells grown on bioactive matrices have immensely advanced many aspects of biomedical research related to drug delivery and tissue engineering. Our main objective was to perform simple evaluation of the structural and biotic qualities of cell scaffolds made of affordable biomaterials for liver cell line (HepG2) cultivation in vitro. In this work the electrospun matrix made of synthetic polyester poly(ε-caprolactone) (PCL) was compared with the natural protein-based extracellular matrix isolated from porcine liver (ECM). Mechanical and structural analysis showed that ECM was about 12 times less resistant to tensile stress while it had significantly larger pore size and twice smaller water contact angle than PCL. Bioactivity assessment included comparison of cell growth and transfection efficiency on cell-seeded scaffolds. Despite the differences in composition and structure between the two respective matrices, the rate of cell spreading and the percentage of transfected cells on both scaffolds were fairly comparable. These results suggest that in an attempt to produce simple, cell carrying structures that adequately simulate the natural scaffold, one can rely on PCL electrospun mats.

Solute diffusion in gels: Thirty years of simulations

In this review, we present a summary of computer simulation studies on solute diffusion in gels carried out in the last three decades. Special attention is paid to coarse-grained simulations in which the role of steric and electrostatic interactions on the particle diffusion can be evaluated. In addition, other important characteristics of particle diffusion in gels, such as the stiffness of the gel structure and hydrodynamic interactions, can be taken into account through coarse-grained simulations. Emphasis is placed on how simulation results help to test phenomenological models and to improve the interpretation interof experimental results. Finally, coarse-grained simulations have also been employed to study the diffusion controlled release of drugs from gels. We believe that scientific advances in this line will be useful to better understand the mechanisms that control the diffusive transport of molecules in a wide variety of biological systems.

Digitally Fabricated and Naturally Augmented In Vitro Tissues

Human in vitro tissues are extracorporeal 3D cultures of human cells embedded in biomaterials, commonly hydrogels, which recapitulate the heterogeneous, multiscale, and architectural environment of the human body. Contemporary strategies used in 3D tissue and organ engineering integrate the use of automated digital manufacturing methods, such as 3D printing, bioprinting, and biofabrication. Human tissues and organs, and their intra- and interphysiological interplay, are particularly intricate. For this reason, attentiveness is rising to intersect materials science, medicine, and biology with arts and informatics. This report presents advances in computational modeling of bioink polymerization and its compatibility with bioprinting, the use of digital design and fabrication in the development of fluidic culture devices, and the employment of generative algorithms for modeling the natural and biological augmentation of in vitro tissues. As a future direction, the use of serially linked in vitro tissues as human body-mimicking systems and their application in drug pharmacokinetics and metabolism, disease modeling, and diagnostics are discussed.

Physical traits of cancer

The role of the physical microenvironment in tumor development, progression, metastasis, and treatment is gaining appreciation. The emerging multidisciplinary field of the physical sciences of cancer is now embraced by engineers, physicists, cell biologists, developmental biologists, tumor biologists, and oncologists attempting to understand how physical parameters and processes affect cancer progression and treatment. Discoveries in this field are starting to be translated into new therapeutic strategies for cancer. In this Review, we propose four physical traits of tumors that contribute to tumor progression and treatment resistance: (i) elevated solid stresses (compression and tension), (ii) elevated interstitial fluid pressure, (iii) altered material properties (for example, increased tissue stiffness, which historically has been used to detect cancer by palpation), and (iv) altered physical microarchitecture. After defining these physical traits, we discuss their causes, consequences, and how they complement the biological hallmarks of cancer.

The Effects of Stiffness, Fluid Viscosity, and Geometry of Microenvironment in Homeostasis, Aging, and Diseases: A Brief Review

Cells sense biophysical cues in the micro-environment and respond to the cues biochemically and biophysically. Proper responses from cells are critical to maintain the homeostasis in the body. Abnormal biophysical cues will cause pathological development in the cells; pathological or aging cells, on the other hand, can alter their micro-environment to become abnormal. In this minireview, we discuss four important biophysical cues of the micro-environment-stiffness, curvature, extracellular matrix (ECM) architecture and viscosity-in terms of their roles in health, aging, and diseases.

A Microscopically Motivated Model for Particle Penetration into Swollen Biological Networks

Biological gels (bio-gels) are hydrated polymer networks that serve diverse biological functions, which often lead to intentional or unintentional exposure to particulate matter. In this work, we derive a microscopically motivated framework that enables the investigation of penetration mechanisms into bio-gels. We distinguish between two types of mechanisms: spontaneous (unforced) penetration and forced penetration. Using experimental data available in the literature, we exploit the proposed model to characterize and compare between the microstructures of respiratory, intestinal, and cervicovaginal mucus and two types of biofilms. Next, we investigate the forced penetration process of spherical and ellipsoidal particles into a locally quadrilateral network. The proposed framework can be used to improve and complement the analysis of experimental findings in vitro, ex vivo, and in vivo. Additionally, the insights from this work pave the way towards enhanced designs of nano-medicines and allow the assessment of risk factors related to the nano-pollutants exposure.

Scale and structure dependent solute diffusivity within microporous tissue engineering scaffolds

Diffusion of nutrients to cells cultured within three-dimensional scaffolds is fundamental for cell survival during development of the tissue construct, when no vasculature is present to aid transport. Significant efforts have been made to characterize the effect of structure on solute diffusivity in nanoporous hydrogels, yet a similar thorough characterization has not been attempted for microporous scaffolds. Here, we make use of freeze-dried collagen scaffolds, possessing pore sizes in the range 150-250 μm and isotropic or aligned morphology, to study the diffusivity of fluorescent dextran molecules. Fluorescence recovery after photobleaching is used to measure the self diffusivity of the solutes within single pores, while Fickian diffusion over scales larger than the pore size is studied by assessing the solute concentration profile within the materials over time. We show that, not only do the morphological parameters of the scaffolds significantly affect the diffusivity of the solutes, but also that the assessment of such diffusivity depends on the length scale of diffusion of the molecules under investigation, with the resulting diffusion coefficients being differently affected by the scaffold structure. The results provided can guide the design of scaffolds with tailored diffusivity and nutrient concentration profiles.

Macromolecular gelatin properties affect fibrin microarchitecture and tumor spheroid behavior in fibrin-gelatin gels

The biophysical properties of extracellular matrices (ECM) are known to regulate cell behavior, however decoupling cell behavior changes due to the relative contributions of material microstructure versus biomechanics or nutrient permeability remains challenging, especially within complex, multi-material matrices. We developed four gelatin-fibrin interpenetrating network (IPN) formulations which are identical in composition but possess variable gelatin molecular weight distributions, and display differences in microstructure, biomechanics, and diffusivity. In this work we interrogate the response of multicellular tumor spheroids to these IPN formulations and found that a high stiffness, gelatin-network dominated IPNs impeded remodeling and invasion of multicellular tumor spheroids; whereas relatively lower stiffness, fibrin-network dominated IPNs permitted protease-dependent remodeling and spheroid invasion. Cell proliferation correlated to nutrient diffusivity across tested IPN formulations. These findings demonstrate the complexity of ECM IPNs, relative to single polymer matrices, and highlight that cell response does not derive from a single aspect of the ECM, but rather from the interplay of multiple biomechanical properties. The methodology developed here represents a framework for future studies which aim to characterize cellular phenotypic responses to biophysical cues present within complex, multi-material matrices.

Active matter therapeutics

Nanotherapies based on micelles, liposomes, polymersomes, nanocapsules, magnetic nanoparticles, and noble metal nanoparticles have been at the forefront of drug delivery in the past few decades. Some of these nanopharmaceuticals have been commercially applied to treat a wide range of diseases, from dry eye syndrome to cancer. However, the majority involve particles that are passive, meaning that they do not change shape, and they lack motility; the static features can limit their therapeutic efficacy. In this review, we take a critical look at an emerging field that seeks to utilize active matter for therapeutics. In this context, active matter can be broadly referred to as micro or nanosized constructs that energetically react with their environment or external fields and translate, rotate, vibrate or change shape. Essentially, the recent literature suggests that such particles could significantly augment present-day drug delivery, by enhancing transport and increasing permeability across anatomical barriers by transporting drugs within solid tumor microenvironments or disrupting cardiovascular plaque. We discuss examples of such particles and link the transport and permeability properties of active matter to potential therapeutic applications in the context of two major diseases, namely cancer and heart disease. We also discuss potential challenges, opportunities, and translational hurdles.

A mathematical model to predict nanomedicine pharmacokinetics and tumor delivery

Towards clinical translation of cancer nanomedicine, it is important to systematically investigate the various parameters related to nanoparticle (NP) physicochemical properties, tumor characteristics, and inter-individual variability that affect the tumor delivery efficiency of therapeutic nanomaterials. Comprehensive investigation of these parameters using traditional experimental approaches is impractical due to the vast parameter space; mathematical models provide a more tractable approach to navigate through such a multidimensional space. To this end, we have developed a predictive mathematical model of whole-body NP pharmacokinetics and their tumor delivery in vivo, and have conducted local and global sensitivity analyses to identify the factors that result in low tumor delivery efficiency and high off-target accumulation of NPs. Our analyses reveal that NP degradation rate, tumor blood viscosity, NP size, tumor vascular fraction, and tumor vascular porosity are the key parameters in governing NP kinetics in the tumor interstitium. The impact of these parameters on tumor delivery efficiency of NPs is discussed, and optimal values for maximizing NP delivery are presented.

Integrated Biophysical Characterization of Fibrillar Collagen-Based Hydrogels

This paper describes an experimental characterization scheme of the biophysical properties of reconstituted hydrogel matrices based on indentation testing, quantification of transport via microfluidics, and confocal reflectance microscopy analysis. While methods for characterizing hydrogels exist and are widely used, they often do not measure diffusive and convective transport concurrently, determine the relationship between microstructure and transport properties, and decouple matrix mechanics and transport properties. Our integrated approach enabled independent and quantitative measurements of the structural, mechanical, and transport properties of hydrogels in a single study. We used fibrillar type I collagen as the base matrix and investigated the effects of two different matrix modifications: (1) cross-linking with human recombinant tissue transglutaminase II (hrTGII) and (2) supplementation with the nonfibrillar matrix constituent hyaluronic acid (HA). hrTGII modified the matrix structure and transport but not mechanical parameters. Furthermore, changes in the matrix structure due to hrTGII were seen to be dependent on the concentration of collagen. In contrast, supplementation of HA at different collagen concentrations altered the matrix microstructure and mechanical indentation behavior but not transport parameters. These experimental observations reveal the important relationship between extracellular matrix (ECM) composition and biophysical properties. The integrated techniques are versatile, robust, and accessible; and as matrix-cell interactions are instrumental for many biological processes, the methods and findings described here should be broadly applicable for characterizing hydrogel materials used for three-dimensional (3-D) tissue-engineered culture models.

Advances in mathematical models of the active targeting of tumor cells by functional nanoparticles

BACKGROUND AND OBJECTIVE

The process of nanoparticles (NPs) entering blood circulation to actively target tumor cells involves four stages-the transport of NPs in blood vessels, transvascular transport of NPs, transport of NPs in the tumor interstitial matrix and entry of NPs into tumor cells. These four stages are a complex process involving mechanical, physical, biochemical, and biophysical factors, the tumor microenvironment (TME) and properties of NPs play important roles in this process. Because this process involves a large number of factors and is very complex, it is difficult to study with conventional methods.

METHODS

Using mathematical models for simulation is suitable for addressing this complex situation and can describe the complexity well.

RESULTS

This work focuses on the theoretical simulation of NPs that target tumor cells to illustrate the effects of the abnormal microenvironment of tumors and properties of NPs on the transport process. Mathematical models constructed by different methods are enumerated. Through studying these mathematical models, different methods to overcome nanoparticle (NP) transport obstacles are illustrated.

CONCLUSIONS

It is necessary to construct a theoretical model of active targeting nanodrug delivery under the coupling of micro-flow field and specific binding force field, and to simulate and analyze the delivery process at mesoscopic scale using computational fluid dynamics (CFD) method, so as to reveal the law and characteristics of drug delivery and cell uptake in the micro-environment of tumors in vivo. The methods and techniques discussed can serve as the basis for systematic studies of active targeting of functional nanoparticles to tumor cells.

Development of a Physiologically-Based Mathematical Model for Quantifying Nanoparticle Distribution in Tumors

Nanomedicine holds promise for the treatment of cancer, as it enables tumor-targeted drug delivery. However, reports on translation of most nanomedicine strategies to the clinic so far have been less than satisfactory, in part due to insufficient understanding of the effects of nanoparticle (NP) physiochemical properties and physiological variables on their pharmacological behavior. In this paper, we present a multiscale mathematical model to examine the efficacy of NP delivery to solid tumors; as a case example, we apply the model to a clinically detectable primary pancreatic ductal adenocarcinoma (PDAC) to assess tissue-scale spatiotemporal distribution profiles of NPs. We integrate NP systemic disposition kinetics with NP-cell interactions in PDAC abstractly described as a two-dimensional structure, which is then parameterized with human physiological data obtained from published literature. Through model analysis of delivery efficiency, we verify the multiscale approach by showing that NP concentration kinetics of interest in various compartments predicted by the whole-body scale model were in agreement with those obtained from the tissue-scale model. We also found that more NPs were trapped in the outer well-perfused tumor region than the inner semi-necrotic domain. Further development of the model may provide a useful tool for optimal NP design and physiological interventions.

Force-dependent extracellular matrix remodeling by early-stage cancer cells alters diffusion and induces carcinoma-associated fibroblasts

It is known cancer cells secrete cytokines inducing normal fibroblasts (NFs) to become carcinoma-associated fibroblasts (CAFs). However, it is not clear how the CAF-promoting cytokines can effectively navigate the dense ECM, a diffusion barrier, in the tumor microenvironment to reach NFs during the early stages of cancer development. In this study, we devised a 3D coculture system to investigate the possible mechanism of CAF induction at early stages of breast cancer. We found that in a force-dependent manner, ECM fibrils are radially aligned relative to the tumor spheroid. The fibril alignment enhances the diffusion of exosomes containing CAF-promoting cytokines towards NFs. Suppression of force generation or ECM remodeling abolishes the enhancement of exosome diffusion and the subsequent CAF induction. In summary, our finding suggests that early-stage, pre-metastatic cancer cells can generate high forces to align the ECM fibrils, thereby enhancing the diffusion of CAF-promoting exosomes to reach the stroma and induce CAFs.

Mechanical Interaction between Cells Facilitates Molecular Transport

In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at the nanometer scale diffuse. The ECM is continuously remodeled by cells, via mechanical interactions, which lead to a potential link between biomechanical and biochemical cell-cell interactions. Here, it is studied how cell-induced forces applied on the ECM impact the biochemical transport of molecules between distant cells. It is experimentally observed that cells remodel the ECM by increasing fiber alignment and density of the matrix between them over time. Using random walk simulations on a 3D lattice, elongated fixed obstacles are implemented that mimic the fibrous ECM structure. Both diffusion of a tracer molecule and the mean first-passage time a molecule secreted from one cell takes to reach another cell are measured. The model predicts that cell-induced remodeling can lead to a dramatic speedup in the transport of molecules between cells. Fiber alignment and densification cause reduction of the transport dimensionality from a 3D to a much more rapid 1D process. Thus, a novel mechanism of mechano-biochemical feedback in the regulation of long-range cell-cell communication is suggested.

Nanoparticle Optimization for Enhanced Targeted Anticancer Drug Delivery

Nanoparticle (NP)-based drug delivery is a promising method to increase the therapeutic index of anticancer agents with low median toxic dose. The delivery efficiency, corresponding to the fraction of the injected NPs that adhere to the tumor site, depends on NP size a and aspect ratio AR. Values for these variables are currently chosen empirically, which may not result in optimal targeted drug delivery. This study applies rigorous optimization to the design of NPs. A preliminary investigation revealed that delivery efficiency increases monotonically with a and AR. However, maximizing a and AR results in nonuniform drug distribution, which impairs tumor regression. Therefore, a multiobjective optimization (MO) problem is formulated to quantify the trade-off between NPs accumulation and distribution. The MO is solved using the derivative-free mesh adaptive direct search algorithm. Theoretically, the Pareto-optimal set consists of an infinite number of mathematically equivalent solutions to the MO problem. However, interesting design solutions can be identified subjectively, e.g., the ellipsoid with a major axis of 720 nm and an aspect ratio of 7.45, as the solution closest to the utopia point. The MO problem formulation is then extended to optimize NP biochemical properties: ligand-receptor binding affinity and ligand density. Optimizing physical and chemical properties simultaneously results in optimal designs with reduced NP sizes and thus enhanced cellular uptake. The presented study provides an insight into NP structures that have potential for producing desirable drug delivery.

Second-harmonic generation directionality is associated with neoadjuvant chemotherapy response in breast cancer core needle biopsies

Neoadjuvant chemotherapy (NACT) is routinely administered to subsets of breast cancer patients, including triple negative (TN) or human epidermal growth factor receptor 2-positive (HER2+) cancers. After NACT and subsequent surgical resection, 5% to 30% of patients have no residual invasive carcinoma, termed pathological complete response. Unfortunately, many patients experience little-to-no response after NACT and unnecessarily suffer its side effects. Methods are needed to predict an individual patient’s response to NACT. Core needle biopsies, taken before NACT, consist of tumor cells and the surrounding extracellular matrix. We performed second-harmonic generation (SHG) imaging of fibrillar collagen in core needle biopsy sections as a possible predictor of response to NACT. The ratio of forward-to-backward scattering (F/B) SHG was assessed in the “tumor bulk” and “tumor–host interface” in HER2+ and TN core needle biopsy sections. Patient response was classified post-treatment using the Residual Cancer Burden (RCB) score. In HER2+ biopsies, RCB class was associated with F/B derived from the tumor–stromal interface, but not tumor bulk. F/B was not associated with RCB class in TN biopsies. These findings suggest that F/B from needle biopsy sections may be a useful predictor of which patients will respond favorably to NACT, with the potential to help reduce overtreatment.

Influence of Tissue Anisotropy on Molecular Communication

Many biological tissues inside the human body exhibit highly anisotropic diffusion properties; for example, tissues of the nervous system and white matter in the brain. Here, we present an improved stochastic molecular communication framework to model interaction between bionanomachines in three-dimensional (3D) anisotropic brain micro-environment. The results obtained using stochastic particle-based simulation model are validated with analytical expressions. We also derive expressions for peak amplitude and peak time for the received molecular signal. The results demonstrate that the channel impulse response in anisotropic biological media depends significantly on the diffusion tensor as well as on the locations of the nanomachines.