Microfluidics for cell-cell interactions: A review

Optimization of Helicobacter pylori Biofilm Formation in In Vitro Conditions Mimicking Stomach

Helicobacter pylori is one of the most common bacterial pathogens worldwide and the main etiological agent of numerous gastric diseases. The frequency of multidrug resistance of H. pylori is growing and the leading factor related to this phenomenon is its ability to form biofilm. Therefore, the establishment of a proper model to study this structure is of critical need. In response to this, the aim of this original article is to validate conditions of the optimal biofilm development of H. pylori in monoculture and co-culture with a gastric cell line in media simulating human fluids. Using a set of culture-based and microscopic techniques, we proved that simulated transcellular fluid and simulated gastric fluid, when applied in appropriate concentrations, stimulate autoaggregation and biofilm formation of H. pylori. Additionally, using a co-culture system on semi-permeable membranes in media imitating the stomach environment, we were able to obtain a monolayer of a gastric cell line with H. pylori biofilm on its surface. We believe that the current model for H. pylori biofilm formation in monoculture and co-culture with gastric cells in media containing host-mimicking fluids will constitute a platform for the intensification of research on H. pylori biofilms in in vitro conditions that simulate the human body.

A microfluidic organ-on-a-chip: into the next decade of bone tissue engineering applied in dentistry

A comprehensive understanding of the complex physiological and pathological processes associated with alveolar bones, their responses to different therapeutics strategies, and cell interactions with biomaterial becomes necessary in precisely treating patients with severe progressive periodontitis, as a bone-related issue in dentistry. However, existing monolayer cell culture or pre-clinical models have been unable to mimic the complex physiological, pathological and regeneration processes in the bone microenvironment in response to different therapeutic strategies. In this point, 'organ-on-a-chip' (OOAC) technology, specifically 'alveolar-bone-on-a-chip', is expected to resolve the problems by better imitating infection site microenvironment and microphysiology within the oral tissues. The OOAC technology is assessed in this study toward better approaches in disease modeling and better therapeutics strategy for bone tissue engineering applied in dentistry.

Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data

BACKGROUND

Complex biological systems are described as a multitude of cell-cell interactions (CCIs). Recent single-cell RNA-sequencing studies focus on CCIs based on ligand-receptor (L-R) gene co-expression but the analytical methods are not appropriate to detect many-to-many CCIs.

RESULTS

In this work, we propose scTensor, a novel method for extracting representative triadic relationships (or hypergraphs), which include ligand-expression, receptor-expression, and related L-R pairs.

CONCLUSIONS

Through extensive studies with simulated and empirical datasets, we have shown that scTensor can detect some hypergraphs that cannot be detected using conventional CCI detection methods, especially when they include many-to-many relationships. scTensor is implemented as a freely available R/Bioconductor package.

Microfluidic systems for particle capture and release: A review

Microfluidic technology has emerged as a promising tool in various applications, including biosensing, disease diagnosis, and environmental monitoring. One of the notable features of microfluidic devices is their ability to selectively capture and release specific cells, biomolecules, bacteria, and particles. Compared to traditional bulk analysis instruments, microfluidic capture-and-release platforms offer several advantages, such as contactless operation, label-free detection, high accuracy, good sensitivity, and minimal reagent requirements. However, despite significant efforts dedicated to developing innovative capture mechanisms in the past, the release and recovery efficiency of trapped particles have often been overlooked. Many previous studies have focused primarily on particle capture techniques and their efficiency, disregarding the crucial role of successful particle release for subsequent analysis. In reality, the ability to effectively release trapped particles is particularly essential to ensure ongoing, high-throughput analysis. To address this gap, this review aims to highlight the importance of both capture and release mechanisms in microfluidic systems and assess their effectiveness. The methods are classified into two categories: those based on physical principles and those using biochemical approaches. Furthermore, the review offers a comprehensive summary of recent applications of microfluidic platforms specifically designed for particle capture and release. It outlines the designs and performance of these devices, highlighting their advantages and limitations in various target applications and purposes. Finally, the review concludes with discussions on the current challenges faced in the field and presents potential future directions.

Cell pairing for biological analysis in microfluidic devices

Cell pairing at the single-cell level usually allows a few cells to contact or seal in a single chamber and provides high-resolution imaging. It is pivotal for biological research, including understanding basic cell functions, creating cancer treatment technologies, developing drugs, and more. Laboratory chips based on microfluidics have been widely used to trap, immobilize, and analyze cells due to their high efficiency, high throughput, and good biocompatibility properties. Cell pairing technology in microfluidic devices provides spatiotemporal research on cellular interactions and a highly controlled approach for cell heterogeneity studies. In the last few decades, many researchers have emphasized cell pairing research based on microfluidics. They designed various microfluidic device structures for different biological applications. Herein, we describe the current physical methods of microfluidic devices to trap cell pairs. We emphatically summarize the practical applications of cell pairing in microfluidic devices, including cell fusion, cell immunity, gap junction intercellular communication, cell co-culture, and other applications. Finally, we review the advances and existing challenges of the presented devices and then discuss the possible development directions to promote medical and biological research.

An open microfluidic coculture model of fibroblasts and eosinophils to investigate mechanisms of airway inflammation

Interactions between fibroblasts and immune cells play an important role in tissue inflammation. Previous studies have found that eosinophils activated with interleukin-3 (IL-3) degranulate on aggregated immunoglobulin G (IgG) and release mediators that activate fibroblasts in the lung. However, these studies were done with eosinophil-conditioned media that have the capacity to investigate only one-way signaling from eosinophils to fibroblasts. Here, we demonstrate a coculture model of primary normal human lung fibroblasts (HLFs) and human blood eosinophils from patients with allergy and asthma using an open microfluidic coculture device. In our device, the two types of cells can communicate via two-way soluble factor signaling in the shared media while being physically separated by a half wall. Initially, we assessed the level of eosinophil degranulation by their release of eosinophil-derived neurotoxin (EDN). Next, we analyzed the inflammation-associated genes and soluble factors using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and multiplex immunoassays, respectively. Our results suggest an induction of a proinflammatory fibroblast phenotype of HLFs following the coculture with degranulating eosinophils, validating our previous findings. Additionally, we present a new result that indicate potential impacts of activated HLFs back on eosinophils. This open microfluidic coculture platform provides unique opportunities to investigate the intercellular signaling between the two cell types and their roles in airway inflammation and remodeling.

Organ-on-a-chip platforms as novel advancements for studying heterogeneity, metastasis, and drug efficacy in breast cancer

Breast cancer has the highest cancer incidence rate in women worldwide. Therapies for breast cancer have shown high success rates, yet many cases of recurrence and drug resistance are still reported. Developing innovative strategies for studying breast cancer may improve therapeutic outcomes of the disease by providing better insight into the associated molecular mechanisms. A novel advancement in breast cancer research is the utilization of organ-on-a-chip (OOAC) technology to establish in vitro physiologically relevant breast cancer biomimetic models. This emerging technology combines microfluidics and tissue culturing methods to establish organ-specific micro fabricated culture models. Here, we shed light on the advantages of OOAC platforms over conventional in vivo and in vitro models in terms of mimicking tissue heterogeneity, disease progression, and facilitating pharmacological drug testing with a focus on models of the mammary gland in both normal and breast cancer states. By highlighting the various designs and applications of the breast-on-a-chip platforms, we show that the latter propose means to facilitate breast cancer-related studies and provide an efficient approach for therapeutic drug screening in vitro.

A Temperature-Based Easy-Separable (TempEasy) 3D Hydrogel Coculture System

Interactions between different cell types are crucial for their behavior in tissues, but are rarely considered in 3D in vitro cell culture experiments. One reason is that such coculture experiments are sometimes difficult to perform in 3D or require specialized equipment or know-how. Here, a new 3D cell coculture system is introduced, TempEasy, which is readily applied in any cell culture lab. The matrix material is based on polyisocyanide hydrogels, which closely resemble the mechanical characteristics of the natural extracellular matrix. Gels with different gelation temperatures, seeded with different cells, are placed on top of each other to form an indirect coculture. Cooling reverses gelation, allowing cell harvesting from each layer separately, which benefits downstream analysis. To demonstrate the potential of TempEasy , human adipose stem cells (hADSCs) with vaginal epithelial fibroblasts are cocultured. The analysis of a 7-day coculture shows that hADSCs promote cell-cell interaction of fibroblasts, while fibroblasts promote proliferation and differentiation of hADSCs. TempEasy provides a straightforward operational platform for indirect cocultures of cells of different lineages in well-defined microenvironments.

Appreciating the role of cell shape changes in the mechanobiology of epithelial tissues

The wide range of epithelial cell shapes reveals the complexity and diversity of the intracellular mechanisms that serve to construct their morphology and regulate their functions. Using mechanosensitive steps, epithelial cells can sense a variety of different mechanochemical stimuli and adapt their behavior by reshaping their morphology. These changes of cell shape rely on a structural reorganization in space and time that generates modifications of the tensional state and activates biochemical cascades. Recent studies have started to unveil how the cell shape maintenance is involved in mechanical homeostatic tasks to sustain epithelial tissue folding, identity, and self-renewal. Here, we review relevant works that integrated mechanobiology to elucidate some of the core principles of how cell shape may be conveyed into spatial information to guide collective processes such as epithelial morphogenesis. Among many other parameters, we show that the regulation of the cell shape can be understood as the result of the interplay between two counteracting mechanisms: actomyosin contractility and intercellular adhesions, and that both do not act independently but are functionally integrated to operate on molecular, cellular, and tissue scales. We highlight the role of cadherin-based adhesions in force-sensing and mechanotransduction, and we report recent developments that exploit physics of liquid crystals to connect cell shape changes to orientational order in cell aggregates. Finally, we emphasize that the further intermingling of different disciplines to develop new mechanobiology assays will lead the way toward a unified picture of the contribution of cell shape to the pathophysiological behavior of epithelial tissues.

Understanding, engineering, and modulating the growth of neural networks: An interdisciplinary approach

A deeper understanding of the brain and its function remains one of the most significant scientific challenges. It not only is required to find cures for a plethora of brain-related diseases and injuries but also opens up possibilities for achieving technological wonders, such as brain-machine interface and highly energy-efficient computing devices. Central to the brain's function is its basic functioning unit (i.e., the neuron). There has been a tremendous effort to understand the underlying mechanisms of neuronal growth on both biochemical and biophysical levels. In the past decade, this increased understanding has led to the possibility of controlling and modulating neuronal growth in vitro through external chemical and physical methods. We provide a detailed overview of the most fundamental aspects of neuronal growth and discuss how researchers are using interdisciplinary ideas to engineer neuronal networks in vitro. We first discuss the biochemical and biophysical mechanisms of neuronal growth as we stress the fact that the biochemical or biophysical processes during neuronal growth are not independent of each other but, rather, are complementary. Next, we discuss how utilizing these fundamental mechanisms can enable control over neuronal growth for advanced neuroengineering and biomedical applications. At the end of this review, we discuss some of the open questions and our perspectives on the challenges and possibilities related to controlling and engineering the growth of neuronal networks, specifically in relation to the materials, substrates, model systems, modulation techniques, data science, and artificial intelligence.

Development and application of a cultivation platform for mammalian suspension cell lines with single-cell resolution

In bioproduction processes, cellular heterogeneity can cause unpredictable process outcomes or even provoke process failure. Still, cellular heterogeneity is not examined systematically in bioprocess research and development. One reason for this shortcoming is the applied average bulk analyses, which are not able to detect cell-to-cell differences. In this study, we present a microfluidic tool for mammalian single-cell cultivation (MaSC) of suspension cells. The design of our platform allows cultivation in highly controllable environments. As a model system, Chinese hamster ovary cells (CHO-K1) were cultivated over 150 h. Growth behavior was analyzed on a single-cell level and resulted in growth rates between 0.85 and 1.16 day^-1 . At the same time, heterogeneous growth and division behavior, for example, unequal division time, as well as rare cellular events like polynucleation or reversed mitosis were observed, which would have remained undetected in a standard population analysis based on average measurements. Therefore, MaSC will open the door for systematic single-cell analysis of mammalian suspension cells. Possible fields of application represent basic research topics like cell-to-cell heterogeneity, clonal stability, pharmaceutical drug screening, and stem cell research, as well as bioprocess related topics such as media development and novel scale-down approaches.

Applications of Gelatin Methacryloyl (GelMA) Hydrogels in Microfluidic Technique-Assisted Tissue Engineering

In recent years, the microfluidic technique has been widely used in the field of tissue engineering. Possessing the advantages of large-scale integration and flexible manipulation, microfluidic devices may serve as the production line of building blocks and the microenvironment simulator in tissue engineering. Additionally, in microfluidic technique-assisted tissue engineering, various biomaterials are desired to fabricate the tissue mimicking or repairing structures (i.e., particles, fibers, and scaffolds). Among the materials, gelatin methacrylate (GelMA)-based hydrogels have shown great potential due to their biocompatibility and mechanical tenability. In this work, applications of GelMA hydrogels in microfluidic technique-assisted tissue engineering are reviewed mainly from two viewpoints: Serving as raw materials for microfluidic fabrication of building blocks in tissue engineering and the simulation units in microfluidic chip-based microenvironment-mimicking devices. In addition, challenges and outlooks of the exploration of GelMA hydrogels in tissue engineering applications are proposed.

Microfluidic device performing on flow study of serial cell–cell interactions of two cell populations

In this study we present a novel microfluidic hydrodynamic trapping device to probe the cell–cell interaction between all cell samples of two distinct populations. We have exploited an hydrodynamic trapping method using microfluidics to immobilize a batch of cells from the first population at specific locations, then relied on hydrodynamic filtering principles, the flowing cells from the second cell population are placed in contact with the trapped ones, through a roll-over mechanism. The rolling cells interact with the serially trapped cells one after the other. The proposed microfluidic phenomenon was characterized with beads. We have shown the validity of our method by detecting the capacity of olfactory receptors to induce adhesion of cell doublets overexpressing these receptors. We report here the first controlled on-flow single cell resolution cell–cell interaction assay in a microfluidic device for future application in cell–cell interactions-based cell library screenings.

In this study we present a novel microfluidic hydrodynamic trapping device to probe the cell–cell interaction between all cell samples of two distinct populations.

Advancements and Potential Applications of Microfluidic Approaches—A Review

A micro-level technique so-called “microfluidic technology or simply microfluidic” has gained a special place as a powerful tool in bioengineering and biomedical engineering research due to its core advantages in modern science and engineering. Microfluidic technology has played a substantial role in numerous applications with special reference to bioscience, biomedical and biotechnological research. It has facilitated noteworthy development in various sectors of bio-research and upsurges the efficacy of research at the molecular level, in recent years. Microfluidic technology can manipulate sample volumes with precise control outside cellular microenvironment, at micro-level. Thus, enable the reduction of discrepancies between in vivo and in vitro environments and reduce the overall reaction time and cost. In this review, we discuss various integrations of microfluidic technologies into biotechnology and its paradigmatic significance in bio-research, supporting mechanical and chemical in vitro cellular microenvironment. Furthermore, specific innovations related to the application of microfluidics to advance microbial life, solitary and co-cultures along with a multiple-type cell culturing, cellular communications, cellular interactions, and population dynamics are also discussed.

Core microbiomes for sustainable agroecosystems

In an era of ecosystem degradation and climate change, maximizing microbial functions in agroecosystems has become a prerequisite for the future of global agriculture. However, managing species-rich communities of plant-associated microbiomes remains a major challenge. Here, we propose interdisciplinary research strategies to optimize microbiome functions in agroecosystems. Informatics now allows us to identify members and characteristics of 'core microbiomes', which may be deployed to organize otherwise uncontrollable dynamics of resident microbiomes. Integration of microfluidics, robotics and machine learning provides novel ways to capitalize on core microbiomes for increasing resource-efficiency and stress-resistance of agroecosystems.

Recent advances in microfluidic technologies for cell-to-cell interaction studies

Microfluidic cell cultures are ideally positioned to become the next generation of in vitro diagnostic tools for biomedical research, where key biological processes such as cell signalling and dynamic cell-to-cell interactions can be reliably analysed under reproducible physiological cell culture conditions. In the last decade, a large number of microfluidic cell analysis systems have been developed for a variety of applications including drug target optimization, drug screening and toxicological testing. More recently, advanced in vitro microfluidic cell culture systems have emerged that are capable of replicating the complex three-dimensional architectures of tissues and organs and thus represent valid biological models for investigating the mechanism and function of human tissue structures, as well as studying the onset and progression of diseases such as cancer. In this review, we present the most important developments in single-cell, 2D and 3D microfluidic cell culture systems for studying cell-to-cell interactions published over the last 6 years, with a focus on cancer research and immunotherapy, vascular models and neuroscience. In addition, the current technological development of microdevices with more advanced physiological cell microenvironments that integrate multiple organ models, namely, the so-called body-, human- and multi-organ-on-a-chip, is reviewed.

Build your own soil: exploring microfluidics to create microbial habitat structures

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.

Generation and manipulation of hydrogel microcapsules by droplet-based microfluidics for mammalian cell culture

Hydrogel microcapsules provide miniaturized and biocompatible niches for three-dimensional (3D) in vitro cell culture. They can be easily generated by droplet-based microfluidics with tunable size, morphology, and biochemical properties. Therefore, microfluidic generation and manipulation of cell-laden microcapsules can be used for 3D cell culture to mimic the in vivo environment towards applications in tissue engineering and high throughput drug screening. In this review of recent advances mainly since 2010, we will first introduce general characteristics of droplet-based microfluidic devices for cell encapsulation with an emphasis on the fluid dynamics of droplet breakup and internal mixing as they directly influence microcapsule's size and structure. We will then discuss two on-chip manipulation strategies: sorting and extraction from oil into aqueous phase, which can be integrated into droplet-based microfluidics and significantly improve the qualities of cell-laden hydrogel microcapsules. Finally, we will review various applications of hydrogel microencapsulation for 3D in vitro culture on cell growth and proliferation, stem cell differentiation, tissue development, and co-culture of different types of cells.

Design of biomimetic cellular scaffolds for co-culture system and their application

The extracellular matrix of most natural tissues comprises various types of cells, including fibroblasts, stem cells, and endothelial cells, which communicate with each other directly or indirectly to regulate matrix production and cell functionality. To engineer multicellular interactions in vitro, co-culture systems have achieved tremendous success achieving a more realistic microenvironment of in vivo metabolism than monoculture system in the past several decades. Recently, the fields of tissue engineering and regenerative medicine have primarily focused on three-dimensional co-culture systems using cellular scaffolds, because of their physical and biological relevance to the extracellular matrix of actual tissues. This review discusses several materials and methods to create co-culture systems, including hydrogels, electrospun fibers, microfluidic devices, and patterning for biomimetic co-culture system and their applications for specific tissue regeneration. Consequently, we believe that culture systems with appropriate physical and biochemical properties should be developed, and direct or indirect cell-cell interactions in the remodeled tissue must be considered to obtain an optimal tissue-specific microenvironment.

Living Cell Microarrays: An Overview of Concepts

Living cell microarrays are a highly efficient cellular screening system. Due to the low number of cells required per spot, cell microarrays enable the use of primary and stem cells and provide resolution close to the single-cell level. Apart from a variety of conventional static designs, microfluidic microarray systems have also been established. An alternative format is a microarray consisting of three-dimensional cell constructs ranging from cell spheroids to cells encapsulated in hydrogel. These systems provide an in vivo-like microenvironment and are preferably used for the investigation of cellular physiology, cytotoxicity, and drug screening. Thus, many different high-tech microarray platforms are currently available. Disadvantages of many systems include their high cost, the requirement of specialized equipment for their manufacture, and the poor comparability of results between different platforms. In this article, we provide an overview of static, microfluidic, and 3D cell microarrays. In addition, we describe a simple method for the printing of living cell microarrays on modified microscope glass slides using standard DNA microarray equipment available in most laboratories. Applications in research and diagnostics are discussed, e.g., the selective and sensitive detection of biomarkers. Finally, we highlight current limitations and the future prospects of living cell microarrays.