Multiscale computational model of fluid flow and matrix deformation in decellularized liver

Strategies for decellularization, re-cellularIzation and crosslinking in liver bioengineering

Liver transplantation is the only definitive treatment for end-stage liver disease and its availability is restricted by organ donor shortages. The development of liver bioengineering provides the probability to create a functional alternative to reduce the gap in organ demand and supply. Decellularized liver scaffolds have been widely applied in bioengineering because they can mimic the native liver microenvironment and retain extracellular matrix (ECM) components. Multiple approaches including chemical, physical and biological methods have been developed for liver decellularization in current studies, but a full set of unified criteria has not yet been established. Each method has its advantages and drawbacks that influence the microstructure and ligand landscape of decellularized liver scaffolds. Optimizing a decellularization method to eliminate cell material while retaining as much of the ECM intact as possible is therefore important for biological scaffold applications. Furthermore, crosslinking strategies can improve the biological performance of scaffolds, including reinforcing biomechanics, delaying degradation in vivo and reducing immune rejection, which can better promote the integration of re-cellularized scaffolds with host tissue and influence the reconstruction process. In this review, we aim to present the different liver decellularization techniques, the crosslinking methods to improve scaffold characteristics with crosslinking and the preparation of soluble ECM.

Liver fibrosis emulation: Impact of the vascular fibrotic alterations on hemodynamics

The liver circulatory system comprises two blood supply vascular trees (the hepatic artery and portal venous networks), microcirculation through the hepatic capillaries (the sinusoids), and a blood drainage vascular tree (the hepatic vein network). Vasculature changes due to fibrosis -located predominantly at the microcirculation level- lead to a marked increase in resistance to flow causing an increase in portal pressure (portal hypertension). Here, we present a liver fibrosis/cirrhosis model. We build on our 1D model of the healthy hepatic circulation, which considers the elasticity of the vessels walls and the pulsatile character of blood flow and pressure, and recreate the deteriorated liver vasculature due to fibrosis. We emulate altered sinusoids by fibrous tissue (stiffened, compressed and splitting) and propose boundary conditions to investigate the impact of fibrosis on hemodynamic variables within the organ. We obtain that the sinusoids stiffness leads to changes in the amplitude and shape of the blood flow and pressure waveforms but not in their mean value. For the compressed and splitting sinusoids, we observe significant increases in the mean value and amplitude of the pressure waveform in the altered sinusoids and in the portal venous network. In other words, we obtain the portal hypertension clinically observed in fibrotic/cirrhotic patients. We also study the extent of the spreading fibrosis by performing the structural fibrotic changes in an increasingly number of sinusoids. Finally, we calculate the portal pressure gradient (PPG) in the model and obtain values in agreement with those reported in the literature for fibrotic/cirrhotic patients.

1D-model of the human liver circulatory system

BACKGROUND AND OBJECTIVE

Blood flow rate and pressure can be measured in vivo by invasive and non-invasive techniques in the large vessels of the hepatic vasculature, but it is not possible to do so along the entire liver circulatory system. Here, we develop a novel 1D model of the liver circulatory system to obtain the hemodynamic signals from macrocirculation to microcirculation with a very low computational cost.

METHODS

The model considers structurally well-defined elements that constitute the entire hepatic circulatory system, the hemodynamics (the temporal-dependence of the blood flow rate and pressure), and the elasticity of the vessel walls.

RESULTS

Using flow rate signals from in vivo measurements as inputs in the model, we obtain pressure signals within their physiological range of values. Furthermore, the model allows to get and analyze the blood flow rate and pressure signals along any vessel of the hepatic vasculature. The impact of the elasticity of the different model components on the inlet pressures is also tested.

CONCLUSIONS

A 1D model of the entire blood vascular system of the human liver is presented for the first time. The model allows to obtain the hemodynamic signals along the hepatic vasculature at a low computational cost. The amplitude and shape of the flow and pressure signals has hardly been studied in the small liver vessels. In this sense, the proposed model is a useful non-invasive exploration tool of the characteristics of the hemodynamic signals. In contrast to models that partially address the hepatic vasculature or those using an electrical analogy, the model presented here is made entirely of structurally well-defined elements. Future works will allow to directly emulate structural vascular alterations due to hepatic diseases and studying their impact on pressure and blood flow signals at key locations of the vasculature.

An electrical analog permeability model assessing fluid flow in a decellularized organ

BACKGROUND AND OBJECTIVE

In recellularization, cell-seeding efficiency refers to the uniform distribution of cells across the decellularized organ, which should be enhanced to ensure effective functioning. During cell seeding, flow dynamics influence the distribution of cells because the driving force of cell movement is the fluid force. However, after decellularization, because of flow permeability through the vessel wall, the fluid pressure and velocity in the vessels of vascular trees are significantly reduced compared with those in the native organ, which might affect cell seeding efficiency. Therefore, it is necessary to assess the flow characteristics in the vessels of decellularized organs to select appropriate seeding conditions. Although electrical analog models have been widely used to investigate the flow distribution in organs, current models do not reflect the permeable conditions. This study proposes a model to extend the conventional electrical analog model to simulate the flow characteristics in decellularized organs.

METHODS

A resistor reflecting permeable flow was added to the original electrical analog model to describe the permeable conditions in the decellularized organs. Decellularization and pressure drop measurements of the kidney were also conducted for model development, calibration, and validation. The developed model was then applied to a decellularized kidney to reveal changes in flow characteristics.

RESULTS

The resistance calculation of permeable flow was determined for each generation of vascular trees. The coefficient of permeability can be indicated by the measured flow exiting through the outlet or the pressure drop across the decellularized organ. The developed permeability model had a qualitative and quantitative agreement with the experimental data without calibration. The results of the permeability model for the decellularized kidney indicated significant reductions of up to 70% in the flow rate and pressure of the organ compared to the native kidney.

CONCLUSIONS

The developed model can simulate the flow characteristics in each individual vessel of decellularized organs. The results from the model can be used to assess the optimal flow rate condition for the cell seeding process.

Hierarchical Modeling of the Liver Vascular System

The liver plays a key role in the metabolic homeostasis of the whole organism. To carry out its functions, it is endowed with a peculiar circulatory system, made of three main dendritic flow structures and lobules. Understanding the vascular anatomy of the liver is clinically relevant since various liver pathologies are related to vascular disorders. Here, we develop a novel liver circulation model with a deterministic architecture based on the constructal law of design over the entire scale range (from macrocirculation to microcirculation). In this framework, the liver vascular structure is a combination of superimposed tree-shaped networks and porous system, where the main geometrical features of the dendritic fluid networks and the permeability of the porous medium, are defined from the constructal viewpoint. With this model, we are able to emulate physiological scenarios and to predict changes in blood pressure and flow rates throughout the hepatic vasculature due to resection or thrombosis in certain portions of the organ, simulated as deliberate blockages in the blood supply to these sections. This work sheds light on the critical impact of the vascular network on mechanics-related processes occurring in hepatic diseases, healing and regeneration that involve blood flow redistribution and are at the core of liver resilience.

Identification of tissue sections from decellularized liver scaffolds for repopulation experiments

BACKGROUND

Biological organ engineering is a novel experimental approach to generate functional liver grafts by decellularization and repopulation. Currently, healthy organs of small or large animals and human organs with preexisting liver diseases are used to optimize decellularization and repopulation.However, the effects of morphological changes on allo- and xenogeneic cell-scaffold interactions during repopulation procedure, e.g., using scaffold-sections, are unknown. We present a sequential morphological workflow to identify murine liver scaffold-sections with well-preserved microarchitecture.

METHODS

Native livers (CONT, n = 9) and livers with experimentally induced pathologies (hepatics steatosis: STEA, n = 7; hepatic fibrosis induced by bile duct ligation: BDL, n = 9; nodular regenerative hyperplasia induced by 90% partial hepatectomy: PH, n = 8) were decellularized using SDS and Triton X-100 to generate cell-free scaffolds. Scaffold-sections were assessed using a sequential morphological workflow consisting of macroscopic, microscopic and morphological evaluation: (1) The scaffold was evaluated by a macroscopic decellularization score. (2) Regions without visible tissue remnants were localized for sampling and histological processing. Subsequent microscopical examination served to identify tissue samples without cell remnants. (3) Only cell-free tissue sections were subjected to detailed liver-specific morphological assessment using a histological and immunohistochemical decellularization score.

RESULTS

Decellularization was feasible in 33 livers, which were subjected to the sequential morphological workflow. In 11 of 33 scaffolds we achieved a good macroscopic decellularization result (CONT: 3 scaffolds; STEA: 3 scaffolds; BDL: 3 scaffolds; PH: 2 scaffolds). The microscopic assessment resulted in the selection of 88 cell-free tissue sections (CONT: 15 sections; STEA: 38 sections; BDL: 30 sections; PH: 5 sections). In 27 of those sections we obtained a good histological decellularization result (CONT: 3 sections; STEA: 6 sections; BDL: 17 sections; PH: 1 section). All experimental groups contained sections with a good immunohistochemical decellularization result (CONT: 6 sections; STEA: 5 sections; BDL: 4 sections; PH: 1 section).

DISCUSSION

Decellularization was possible in all experimental groups, irrespectively of the underlying morphological alteration. Furthermore, our proposed sequential morphological workflow was suitable to detect tissue sections with well-preserved hepatic microarchitecture, as needed for further repopulation experiments.

Impact of tumor-parenchyma biomechanics on liver metastatic progression: a multi-model approach

Colorectal cancer and other cancers often metastasize to the liver in later stages of the disease, contributing significantly to patient death. While the biomechanical properties of the liver parenchyma (normal liver tissue) are known to affect tumor cell behavior in primary and metastatic tumors, the role of these properties in driving or inhibiting metastatic inception remains poorly understood, as are the longer-term multicellular dynamics. This study adopts a multi-model approach to study the dynamics of tumor-parenchyma biomechanical interactions during metastatic seeding and growth. We employ a detailed poroviscoelastic model of a liver lobule to study how micrometastases disrupt flow and pressure on short time scales. Results from short-time simulations in detailed single hepatic lobules motivate constitutive relations and biological hypotheses for a minimal agent-based model of metastatic growth in centimeter-scale tissue over months-long time scales. After a parameter space investigation, we find that the balance of basic tumor-parenchyma biomechanical interactions on shorter time scales (adhesion, repulsion, and elastic tissue deformation over minutes) and longer time scales (plastic tissue relaxation over hours) can explain a broad range of behaviors of micrometastases, without the need for complex molecular-scale signaling. These interactions may arrest the growth of micrometastases in a dormant state and prevent newly arriving cancer cells from establishing successful metastatic foci. Moreover, the simulations indicate ways in which dormant tumors could "reawaken" after changes in parenchymal tissue mechanical properties, as may arise during aging or following acute liver illness or injury. We conclude that the proposed modeling approach yields insight into the role of tumor-parenchyma biomechanics in promoting liver metastatic growth, and advances the longer term goal of identifying conditions to clinically arrest and reverse the course of late-stage cancer.

Modeling the initial-volume dependent approximate compressibility of porcine liver tissues using a novel volumetric strain energy model

Experimental observations in the open literature indicate that soft tissues are slightly compressible, and this characteristic affects not only their overall elastic response but also their damage evolution and failure mechanism. In this study, we find that the compressibility of liver tissues is also closely related to the initial specimen volume according to the confined compression tests: the samples with smaller initial volume exhibit more compressible behavior compared to the larger ones. To include this initial-volume dependent effect, we developed a novel volumetric strain energy model with two variables, i.e., the bulk modulus and the compressibility factor. A detailed scheme was proposed as well to identify these two parameters, and the relationship between the bulk modulus and the initial volume was clarified. Findings from this study will help to deepen the understanding of the biomechanical properties of soft tissues. STATEMENT OF SIGNIFICANCE: Liver is a highly vascular organ and traditionally assumed to be an incompressible medium. However, through the confined compression tests, we found that the samples with smaller initial volumes exhibit more compressible behavior. Hence, we developed a novel strain energy density model to characterize the initial-volume dependent hyperelastic response, and found that the bulk modulus of liver tissues is positively related to the initial volume. Our results suggest that the compressibility of liver tissues should be considered in the future study of liver biomechanics.

Modeling of Nanotherapy Response as a Function of the Tumor Microenvironment: Focus on Liver Metastasis

The tumor microenvironment (TME) presents a challenging barrier for effective nanotherapy-mediated drug delivery to solid tumors. In particular for tumors less vascularized than the surrounding normal tissue, as in liver metastases, the structure of the organ itself conjures with cancer-specific behavior to impair drug transport and uptake by cancer cells. Cells and elements in the TME of hypovascularized tumors play a key role in the process of delivery and retention of anti-cancer therapeutics by nanocarriers. This brief review describes the drug transport challenges and how they are being addressed with advanced in vitro 3D tissue models as well as with in silico mathematical modeling. This modeling complements network-oriented techniques, which seek to interpret intra-cellular relevant pathways and signal transduction within cells and with their surrounding microenvironment. With a concerted effort integrating experimental observations with computational analyses spanning from the molecular- to the tissue-scale, the goal of effective nanotherapy customized to patient tumor-specific conditions may be finally realized.

Hydrostatic pressure regulates CYP1A2 expression in human hepatocytes via a mechanosensitive aryl hydrocarbon receptor-dependent pathway

Approximately 75% of xenobiotics are primarily eliminated through metabolism; thus the accurate scaling of metabolic clearance is vital to successful drug development. Yet, when data is scaled from in vitro to in vivo, hepatic metabolic clearance, the primary source of metabolism, is still commonly underpredicted. Over the past decades, with biophysics used as a key component to restore aspects of the in vivo environment, several new cell culture settings have been investigated to improve hepatocyte functionalities. Most of these studies have focused on shear stress, i.e., flow mediated by a pressure gradient. One potential conclusion of these studies is that hepatocytes are naturally "mechanosensitive," i.e., they respond to a change in their biophysical environment. We demonstrate that hepatocytes also respond to an increase in hydrostatic pressure that, we suggest, is directly linked to the lobule geometry and vessel density. Furthermore, we demonstrate that hydrostatic pressure improves albumin production and increases cytochrome P-450 (CYP) 1A2 expression levels in an aryl hydrocarbon-dependent manner in human hepatocytes. Increased albumin production and CYP function are commonly attributed to the impacts of shear stress in microfluidic experiments. Therefore, our results highlight evidence of a novel link between hydrostatic pressure and CYP metabolism and demonstrate that the spectrum of hepatocyte mechanosensitivity might be larger than previously thought.

Construction of sinusoid-scale microvessels in perfusion culture of a decellularized liver

There is a great deal of demand for the construction of transplantable liver grafts. Over the last decade, decellularization techniques have been developed to construct whole liver tissue grafts as potential biomaterials. However, the lack of intact vascular networks, especially sinusoids, in recellularized liver scaffolds leads to hemorrhage and thrombosis after transplantation, which is a major obstacle to the development of transplantable liver grafts. In the present study, we hypothesized that both mechanical (e.g., fluid shear stress) and chemical factors (e.g., fibronectin coating) can enhance the formation of hierarchical vascular networks including sinusoid-scale microvessels. We demonstrated that perfusion culture promoted formation of sinusoid-scale microvessels in recellularized liver scaffolds, which was not observed in static culture. In particular, perfusion culture at 4.7 ml/min promoted the formation of sinusoid-scale microvessels compared to perfusion culture at 2.4 and 9.4 ml/min. In addition, well-aligned endothelium was observed in perfusion culture, suggesting that endothelial cells sensed the flow-induced shear stress. Moreover, fibronectin coating of decellularized liver scaffolds enhanced the formation of sinusoid-scale microvessels in perfusion culture at 4.7 ml/min. This study represents a critical step in the development of functional recellularized liver scaffolds, which can be used not only for transplantation but also for drug screening and disease-modeling studies. STATEMENT OF SIGNIFICANCE: Decellularized liver scaffolds are promising biomaterials that allow production of large-scale tissue-engineered liver grafts. However, it is difficult to maintain recellularized liver grafts after transplantation due to hemorrhage and thrombosis. To overcome this obstacle, construction of an intact vascular network including sinusoid-scale microvessels is essential. In the present study, we succeeded in constructing sinusoid-scale microvessels in decellularized liver scaffolds via a combination of perfusion culture and surface coating. We further confirmed that endothelial cells in decellularized liver scaffolds responded to flow-derived mechanical stress by aligning actin filaments. Our strategy to construct sinusoid-scale microvessels is critical for the development of intact vascular networks, and addresses the limitations of recellularized liver scaffolds after transplantation.

Modeling of xenobiotic transport and metabolism in virtual hepatic lobule models

Computational models of normal liver function and xenobiotic induced liver damage are increasingly being used to interpret in vitro and in vivo data and as an approach to the de novo prediction of the liver’s response to xenobiotics. The microdosimetry (dose at the level of individual cells) of xenobiotics vary spatially within the liver because of both compound-independent and compound-dependent factors. In this paper, we build model liver lobules to investigate the interplay between vascular structure, blood flow and cellular transport that lead to regional variations in microdosimetry. We then compared simulation results obtained using this complex spatial model with a simpler linear pipe model of a sinusoid and a very simple single box model. We found that variations in diffusive transport, transporter-mediated transport and metabolism, coupled with complex liver sinusoid architecture and blood flow distribution, led to three essential patterns of xenobiotic exposure within the virtual liver lobule: (1) lobular-wise uniform, (2) radially varying and (3) both radially and azimuthally varying. We propose to use these essential patterns of exposure as a reference for selection of model representations when a computational study involves modeling detailed hepatic responses to xenobiotics.

Progress Towards Computational 3-D Multicellular Systems Biology

Tumors cannot be understood in isolation from their microenvironment. Tumor and stromal cells change phenotype based upon biochemical and biophysical inputs from their surroundings, even as they interact with and remodel the microenvironment. Cancer should be investigated as an adaptive, multicellular system in a dynamical microenvironment. Computational modeling offers the potential to detangle this complex system, but the modeling platform must ideally account for tumor heterogeneity, substrate and signaling factor biotransport, cell and tissue biophysics, tissue and vascular remodeling, microvascular and interstitial flow, and links between all these sub-systems. Such a platform should leverage high-throughput experimental data, while using open data standards for reproducibility. In this chapter, we review advances by our groups in these key areas, particularly in advanced models of tissue mechanics and interstitial flow, open source simulation software, high-throughput phenotypic screening, and multicellular data standards. In the future, we expect a transformation of computational cancer biology from individual groups modeling isolated parts of cancer, to coalitions of groups combining compatible tools to simulate the 3-D multicellular systems biology of cancer tissues.

A Liver-Centric Multiscale Modeling Framework for Xenobiotics

We describe a multi-scale, liver-centric in silico modeling framework for acetaminophen pharmacology and metabolism. We focus on a computational model to characterize whole body uptake and clearance, liver transport and phase I and phase II metabolism. We do this by incorporating sub-models that span three scales; Physiologically Based Pharmacokinetic (PBPK) modeling of acetaminophen uptake and distribution at the whole body level, cell and blood flow modeling at the tissue/organ level and metabolism at the sub-cellular level. We have used standard modeling modalities at each of the three scales. In particular, we have used the Systems Biology Markup Language (SBML) to create both the whole-body and sub-cellular scales. Our modeling approach allows us to run the individual sub-models separately and allows us to easily exchange models at a particular scale without the need to extensively rework the sub-models at other scales. In addition, the use of SBML greatly facilitates the inclusion of biological annotations directly in the model code. The model was calibrated using human in vivo data for acetaminophen and its sulfate and glucuronate metabolites. We then carried out extensive parameter sensitivity studies including the pairwise interaction of parameters. We also simulated population variation of exposure and sensitivity to acetaminophen. Our modeling framework can be extended to the prediction of liver toxicity following acetaminophen overdose, or used as a general purpose pharmacokinetic model for xenobiotics.