Models of the Gut for Analyzing the Impact of Food and Drugs

Gut-on-a-Chip Research for Drug Development: Implications of Chip Design on Preclinical Oral Bioavailability or Intestinal Disease Studies

The gut plays a key role in drug absorption and metabolism of orally ingested drugs. Additionally, the characterization of intestinal disease processes is increasingly gaining more attention, as gut health is an important contributor to our overall health. The most recent innovation to study intestinal processes in vitro is the development of gut-on-a-chip (GOC) systems. Compared to conventional in vitro models, they offer more translational value, and many different GOC models have been presented over the past years. Herein, we reflect on the almost unlimited choices in designing and selecting a GOC for preclinical drug (or food) development research. Four components that largely influence the GOC design are highlighted, namely (1) the biological research questions, (2) chip fabrication and materials, (3) tissue engineering, and (4) the environmental and biochemical cues to add or measure in the GOC. Examples of GOC studies in the two major areas of preclinical intestinal research are presented: (1) intestinal absorption and metabolism to study the oral bioavailability of compounds, and (2) treatment-orientated research for intestinal diseases. The last section of this review presents an outlook on the limitations to overcome in order to accelerate preclinical GOC research.

Organs-on-chips technologies – A guide from disease models to opportunities for drug development

Current in-vitro 2D cultures and animal models present severe limitations in recapitulating human physiopathology with striking discrepancies in estimating drug efficacy and side effects when compared to human trials. For these reasons, microphysiological systems, organ-on-chip and multiorgans microdevices attracted considerable attention as novel tools for high-throughput and high-content research to achieve an improved understanding of diseases and to accelerate the drug development process towards more precise and eventually personalized standards. This review takes the form of a guide on this fast-growing field, providing useful introduction to major themes and indications for further readings. We start analyzing Organs-on-chips (OOC) technologies for testing the major drug administration routes: (1) oral/rectal route by intestine-on-a-chip, (2) inhalation by lung-on-a-chip, (3) transdermal by skin-on-a-chip and (4) intravenous through vascularization models, considering how drugs penetrate in the bloodstream and are conveyed to their targets. Then, we focus on OOC models for (other) specific organs and diseases: (1) neurodegenerative diseases with brain models and blood brain barriers, (2) tumor models including their vascularization, organoids/spheroids, engineering and screening of antitumor drugs, (3) liver/kidney on chips and multiorgan models for gastrointestinal diseases and metabolic assessment of drugs and (4) biomechanical systems recapitulating heart, muscles and bones structures and related diseases. Successively, we discuss technologies and materials for organ on chips, analyzing (1) microfluidic tools for organs-on-chips, (2) sensor integration for real-time monitoring, (3) materials and (4) cell lines for organs on chips. (Nano)delivery approaches for therapeutics and their on chip assessment are also described. Finally, we conclude with a critical discussion on current significance/relevance, trends, limitations, challenges and future prospects in terms of revolutionary impact on biomedical research, preclinical models and drug development.

The Gut-Organ-Axis Concept: Advances the Application of Gut-on-Chip Technology

The intestine is considered to be a vital digestive organ to absorb nutrients and is the largest immune organ, while numerous microorganisms coexist with the host. It is well known that the complex interactions between the gut microbiota and the host's immune system inevitably affect the function of other organs, creating an "axis" between them. During the past few years, a new technique based mainly on microfluidics and cell biology has been developed to emulate the structure, function, and microenvironment of the human gut, called the "gut-on-chip". This microfluidic chip provides insight into key aspects of gut function in health and disease, such as the gut-brain axis, gut-liver axis, gut-kidney axis, and gut-lung axis. In this review, we first describe the basic theory of the gut axis and the various composition and parameter monitoring of the gut microarray systems, as well as summarize the development and emerging advances in the gut-organ-on-chip, with a focus on the host-gut flora and nutrient metabolism, and highlight their role in pathophysiological studies. In addition, this paper discusses the challenges and prospects for the current development and further use of the gut-organ-on-chip platform.

Gut-on-a-chip for disease models

The intestinal tract is a vital organ responsible for digestion and absorption in the human body and plays an essential role in pathogen invasion. Compared with other traditional models, gut-on-a-chip has many unique advantages, and thereby, it can be considered as a novel model for studying intestinal functions and diseases. Based on the chip design, we can replicate the in vivo microenvironment of the intestine and study the effects of individual variables on the experiment. In recent years, it has been used to study several diseases. To better mimic the intestinal microenvironment, the structure and function of gut-on-a-chip are constantly optimised and improved. Owing to the complexity of the disease mechanism, gut-on-a-chip can be used in conjunction with other organ chips. In this review, we summarise the human intestinal structure and function as well as the development and improvement of gut-on-a-chip. Finally, we present and discuss gut-on-a-chip applications in inflammatory bowel disease (IBD), viral infections and phenylketonuria. Further improvement of the simulation and high throughput of gut-on-a-chip and realisation of personalised treatments are the problems that should be solved for gut-on-a-chip as a disease model.

The translational roadmap of the gut models, focusing on gut-on-chip

It is difficult to model in vitro the intestine when seeking to include crosstalk with the gut microbiota, immune and neuroendocrine systems. Here we present a roadmap of the current models to facilitate the choice in preclinical and translational research with a focus on gut-on-chip. These micro physiological systems (MPS) are microfluidic devices that recapitulate in vitro the physiology of the intestine. We reviewed the gut-on-chips that had been developed in academia and industries as single chip and that have three main purpose: replicate the intestinal physiology, the intestinal pathological features, and for pharmacological tests.

The translational roadmap of the gut models, focusing on gut-on-chip

It is difficult to model in vitro the intestine when seeking to include crosstalk with the gut microbiota, immune and neuroendocrine systems. Here we present a roadmap of the current models to facilitate the choice in preclinical and translational research with a focus on gut-on-chip. These micro physiological systems (MPS) are microfluidic devices that recapitulate in vitro the physiology of the intestine. We reviewed the gut-on-chips that had been developed in academia and industries as single chip and that have three main purpose: replicate the intestinal physiology, the intestinal pathological features, and for pharmacological tests.

PSC-derived intestinal organoids with apical-out orientation as a tool to study nutrient uptake, drug absorption and metabolism

Intestinal organoids recapitulate many features of the in vivo gastrointestinal tract and have revolutionized in vitro studies of intestinal function and disease. However, the restricted accessibility of the apical surface of the organoids facing the central lumen (apical-in) limits studies related to nutrient uptake and drug absorption and metabolism. Here, we demonstrate that pluripotent stem cell (PSC)-derived intestinal organoids with reversed epithelial polarity (apical-out) can successfully recapitulate tissue-specific functions. In particular, these apical-out organoids show strong epithelial barrier formation with all the major junctional complexes, nutrient transport and active lipid metabolism. Furthermore, the organoids express drug-metabolizing enzymes and relevant apical and basolateral transporters. The scalable and robust generation of functional, apical-out intestinal organoids lays the foundation for a completely new range of organoid-based high-throughput/high-content in vitro applications in the fields of nutrition, metabolism and drug discovery.

In silico modeling of endocrine organ-on-a-chip systems

The organ-on-a-chip (OoC) is an artificially reconstructed microphysiological system that is implemented using tissue mimics integrated into miniaturized perfusion devices. OoCs emulate dynamic and physiologically relevant features of the body, which are not available in standard in vitro methods. Furthermore, OoCs provide highly sophisticated multi-organ connectivity and biomechanical cues based on microfluidic platforms. Consequently, they are often considered ideal in vitro systems for mimicking self-regulating biophysical and biochemical networks in vivo where multiple tissues and organs crosstalk through the blood flow, similar to the human endocrine system. Therefore, OoCs have been extensively applied to simulate complex hormone dynamics and endocrine signaling pathways in a mechanistic and fully controlled manner. Mathematical and computational modeling approaches are critical for quantitatively analyzing an OoC and predicting its complex responses. In this review article, recently developed in silico modeling concepts of endocrine OoC systems are summarized, including the mathematical models of tissue-level transport phenomena, microscale fluid dynamics, distant hormone signaling, and heterogeneous cell-cell communication. From this background, whole chip-level analytic approaches in pharmacokinetics and pharmacodynamics will be described with a focus on the spatial and temporal behaviors of absorption, distribution, metabolism, and excretion in endocrine biochips. Finally, quantitative design frameworks for endocrine OoCs are reviewed with respect to support parameter calibration/scaling and enable predictive in vitro-in vivo extrapolations. In particular, we highlight the analytical and numerical modeling strategies of the nonlinear phenomena in endocrine systems on-chip, which are of particular importance in drug screening and environmental health applications.

Organ-on-a-chip: A new tool for in vitro research

Organ-on-a-chip (OOC, organ chip) technology can closely simulate the human microenvironment, synthesize organ-like functional units on a fluidic chip substrate, and simulate the physiology of tissues and organs. It will become an increasingly important platform for in vitro drug development and screening. Most importantly, organ-on-a-chip technology, incorporating 3D cell cultures, overcomes the traditional drawbacks of 2D (flat) cell-culture technology in vitro and in vivo animal trials, neither of which generate completely reliable results when it comes to the actual human subject. It is expected that organ chips will allow huge reductions in the incidence of failure in late-stage human trials, thus slashing the cost of drug development and speeding up the introduction of drugs that are effective. There have been three key enabling technologies that have made organ chip technology possible: 3D bioprinting, fluidic chips, and 3D cell culture, of which the last has allowed cells to be cultivated under more physiologically realistic growth conditions than 2D culture. The fusion of these advanced technologies and the addition of new research methods and algorithms has enabled the construction of chip types with different structures and different uses, providing a wide range of controllable microenvironments, both for research at the cellular level and for more reliable analysis of the action of drugs on the human body. This paper summarizes some research progress of organ-on-a-chip in recent years, outlines the key technologies used and the achievements in drug screening, and makes some suggestions concerning the current challenges and future development of organ-on-a-chip technology.

16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene

Activities of gut microbiomes are often overlooked in assessments of ecotoxicological effects of environmental contaminants. Effects of the polycyclic aromatic hydrocarbon, benzo[a]pyrene (BaP) on active gut microbiomes of juvenile fathead minnows (Pimephales promelas) were investigated. Fish were exposed for two weeks, to concentrations of 0, 1, 10, 100, or 1000 μg BaP g^-1 in the diet. The active gut microbiome was characterized using 16S rRNA metabarcoding to determine its response to dietary exposure of BaP. BaP reduced alpha-diversity at the greatest exposure concentrations. Additionally, exposure to BaP altered community composition of active microbiome and resulted in differential proportion of taxa associated with hydrocarbon degradation and fish health. Neighborhood selection networks of active microbiomes were not reduced with greater concentrations of BaP, which suggests ecological resistance and/or resilience of gut microbiota. The active gut microbiome had a similar overall biodiversity as that of the genomic gut microbiota, but had a distinct composition from that of the 16S rDNA profile. Responses of alpha- and beta-diversities of the active microbiome to BaP exposure were consistent with that of genomic microbiomes. Normalized activity of microbiome via the ratio of rRNA to rDNA abundance revealed rare taxa that became active or dormant due to exposure to BaP. These differences highlight the need to assess both 16S rDNA and rRNA metabarcoding to fully derive bacterial compositional changes resulting from exposure to contaminants.

Dynamic flow and shear stress as key parameters for intestinal cells morphology and polarization in an organ-on-a-chip model

Gut-on-a-chip microfluidic devices have emerged as versatile and practical systems for modeling the human intestine in vitro. Cells cultured under microfluidic conditions experience the effect of shear stress, used as a biomechanical cue to promote a faster cell polarization in Caco-2 cells when compared with static culture conditions. However, published systems to date have utilized a constant flow rate that fails to account for changes in cell shear stress (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\tau }_{c}$$\end{document}τc) resulting from changes in cell elongation that occur with differentiation. In this study, computational fluid dynamics (CFD) simulations predict that cells with villi-like morphology experience a \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\tau }_{c}$$\end{document}τc higher than bulge-like cells at the initial growth stages. Therefore, we investigated the use of a dynamic flow rate to maintain a constant \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\tau }_{c}$$\end{document}τc across the experiment. Microscopic assessment of cell morphology and dome formation confirmed the initiation of Caco-2 polarization within three days. Next, adopting our dynamic approach, we evaluated whether the following decreased flow could still contribute to complete cell differentiation if compared with the standard constant flow methodology. Caco-2 cells polarized under both conditions, secreted mucin-2 and villin and formed tight junctions and crypt-villi structures. Gene expression was not impacted using the dynamic flow rate. In conclusion, our dynamic flow approach still facilitates cell differentiation while enabling a reduced consumption of reagents.

Evaluation of Hybrid Vesicles in an Intestinal Cell Model Based on Structured Paper Chips

Cell culture-based intestinal models are important to evaluate nanoformulations intended for oral drug delivery. We report the use of a floating structured paper chip as a scaffold for Caco-2 cells and HT29-MTX-E12 cells that are two established cell types used in intestinal cell models. The formation of cell monolayers for both mono- and cocultures in the paper chip are confirmed and the level of formed cell-cell junctions is evaluated. Further, cocultures show first mucus formation between 6-10 days with the mucus becoming more pronounced after 19 days. Hybrid vesicles (HVs) made from phospholipids and the amphiphilic block copolymer poly(cholesteryl methacrylate)-block-poly(2-carboxyethyl acrylate) in different ratios are used as a representative soft nanoparticle to assess their mucopenetration ability in paper chip-based cell cultures. The HV assembly is characterized, and it is illustrated that these HVs cross the mucus layer and are found intracellularly within 3 h when the cells are grown in the paper chips. Taken together, the moist three-dimensional cellulose environment of structured paper chips offers an interesting cell culture-based intestinal model that can be further integrated with fluidic systems or online read-out opportunities.

An overview of in vitro, ex vivo and in vivo models for studying the transport of drugs across intestinal barriers

Oral administration is the most commonly used route for drug delivery owing to its cost-effectiveness, ease of administration, and high patient compliance. However, the absorption of orally delivered compounds is a complex process that greatly depends on the interplay between the characteristics of the drug/formulation and the gastrointestinal tract. In this contribution, we review the different preclinical models (in vitro, ex vivo and in vivo) from their development to application for studying the transport of drugs across intestinal barriers. This review also discusses the advantages and disadvantages of each model. Furthermore, the authors have reviewed the selection and validation of these models and how the limitations of the models can be addressed in future investigations. The correlation and predictability of the intestinal transport data from the preclinical models and human data are also explored. With the increasing popularity and prevalence of orally delivered drugs/formulations, sophisticated preclinical models with higher predictive capacity for absorption of oral formulations used in clinical studies will be needed.

In vitro models replicating the human intestinal epithelium for absorption and metabolism studies: A systematic review

Absorption, distribution, metabolism and excretion (ADME) studies represent a fundamental step in the early stages of drug discovery. In particular, the absorption of orally administered drugs, which occurs at the intestinal level, has gained attention since poor oral bioavailability often led to failures for new drug approval. In this context, several in vitro preclinical models have been recently developed and optimized to better resemble human physiology in the lab and serve as an animal alternative to accomplish the 3Rs principles. However, numerous models are ineffective in recapitulating the key features of the human small intestine epithelium and lack of prediction potential for drug absorption and metabolism during the preclinical stage. In this review, we provide an overview of in vitro models aimed at mimicking the intestinal barrier for pharmaceutical screening. After briefly describing how the human small intestine works, we present i) conventional 2D synthetic and cell-based systems, ii) 3D models replicating the main features of the intestinal architecture, iii) micro-physiological systems (MPSs) reproducing the dynamic stimuli to which cells are exposed in the native microenvironment. In this review, we will highlight the benefits and drawbacks of the leading intestinal models used for drug absorption and metabolism studies.

Alternative model organisms for toxicological fingerprinting of relevant parameters in food and nutrition

In the field of (food) toxicology, there is a strong trend of replacing animal trials with alternative methods for the assessment of adverse health effects in humans. The replacement of animal trials is not only driven by ethical concerns but also by the number of potential testing substances (food additives, packaging material, contaminants, and toxicants), which is steadily increasing. In vitro 2D cell culture applications in combination with in silico modeling might provide an applicable first response. However, those systems lack accurate predictions of metabolic actions. Thus, alternative in vivo models could fill the gap between cell culture and animal trials. In this review, we highlight relevant studies in the field and spotlight the applicability of alternative models, including C. elegans, D. rerio, Drosophila, HET-CAM and Lab-on-a-chip.

Rapid Evaluation of Intestinal Paracellular Permeability Using the Human Enterocytic-Like Caco-2/TC7 Cell Line

Paracellular permeability of the intestinal epithelium is a feature of the intestinal barrier, which plays an important role in the physiology of gut and the whole organism. Intestinal paracellular permeability is controlled by complex processes and is involved in the passage of ions and fluids (called pore pathway) and macromolecules (called leak pathway) through tight junctions, which seal the intercellular space. Impairment of intestinal paracellular permeability is associated with several diseases. The identification of a defect in intestinal paracellular permeability may help to understand the implication of gut barrier as a cause or a consequence in human pathology. Here we describe two complementary methods to evaluate alteration of paracellular permeability in cell culture, using the human intestinal cell line Caco-2 and its clone Caco-2/TC7.

Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models

The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.

An Intestine-on-a-Chip Model of Plug-and-Play Modularity to Study Inflammatory Processes

Development of efficient drugs and therapies for the treatment of inflammatory conditions in the intestine is often hampered by the lack of reliable, robust, and high-throughput in vitro and in vivo models. Current models generally fail to recapitulate key aspects of the intestine, resulting in low translatability to the human situation. Here, an immunocompetent 3D perfused intestine-on-a-chip platform was developed and characterized for studying intestinal inflammation. Forty independent polarized 3D perfused epithelial tubular structures were grown from cells of mixed epithelial origin, including enterocytes (Caco-2) and goblet cells (HT29-MTX-E12). Immune cells THP-1 and MUTZ-3, which can be activated, were added to the system and assessed for cytokine release. Intestinal inflammation was mimicked through exposure to tumor necrosis factor-α (TNFα) and interleukin (IL)-1β. The effects were quantified by measuring transepithelial electrical resistance (TEER) and proinflammatory cytokine secretion on the apical and basal sides. Cytokines induced an inflammatory state in the culture, as demonstrated by the impaired barrier function and increased IL-8 secretion. Exposure to the known anti-inflammatory drug TPCA-1 prevented the inflammatory state. The model provides biological modularity for key aspects of intestinal inflammation, making use of well-established cell lines. This allows robust assays that can be tailored in complexity to serve all preclinical stages in the drug discovery and development process.

Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research

The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host-microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host-microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient-microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.

Survival and Germination of Bacillus clausii UBBC07 Spores in in vitro Human Gastrointestinal Tract Simulation Model and Evaluation of Clausin Production

Bacillus clausii UBBC07 is a commercial spore probiotic known to reduce diarrhea in children and adults. In the present study, survival and germination of UBBC07 spores were investigated under fed and fasted conditions in Simulator of Human Intestinal Microbial Ecosystem. Besides this, lantibiotic production, purification, and characterization were performed. The agar plate analysis showed that spores were 100% tolerant to fed and fasted gastrointestinal tract (GIT) conditions. Simultaneously, flow cytometry revealed that at the end of small intestinal incubation, 120% (fed) and 133% (fasted) spores were in viable germinating state. The transformation of viable germinating spores into viable vegetative cells was observed at 3 h of incubation under fasted GIT conditions. In antimicrobial evaluation, UBBC07 produced low-molecular-weight (2107.94 Da) class I lantibiotic clausin. The presence of lanB, lanC, and lanD genes confirms the clausin production. Clausin is stable at proteases (pepsin, proteinase K, and trypsin), temperature (up to 100°C), and pH (up to 11). Furthermore, the antimicrobial activity toward Gram-positive bacteria including Clostridium difficile is advantageous. In conclusion, B. clausii UBBC07 spore probiotic is capable of surviving and germinating under in vitro upper GIT conditions. The clausin production justifies strain applicability in diarrhea.

Orally ingestible medical devices for gut engineering

Orally ingestible medical devices provide significant advancement for diagnosis and treatment of gastrointestinal (GI) tract-related conditions. From micro- to macroscale devices, with designs ranging from very simple to complex, these medical devices can be used for site-directed drug delivery in the GI tract, real-time imaging and sensing of gut biomarkers. Equipped with uni-direction release, or self-propulsion, or origami design, these microdevices are breaking the barriers associated with drug delivery, including biologics, across the GI tract. Further, on-board microelectronics allow imaging and sensing of gut tissue and biomarkers, providing a more comprehensive understanding of underlying pathophysiological conditions. We provide an overview of recent advances in orally ingestible medical devices towards drug delivery, imaging and sensing. Challenges associated with gut microenvironment, together with various activation/actuation modalities of medical devices for micromanipulation of the gut are discussed. We have critically examined the relationship between materials–device design–pharmacological responses with respect to existing regulatory guidelines and provided a clear roadmap for the future.

Simulating human digestion: developing our knowledge to create healthier and more sustainable foods

The gold standard for nutrition studies is clinical trials but they are expensive and variable, and do not always provide the mechanistic information required, hence the increased use ofin vitroand increasinglyin silicosimulations of digestion.