Hierarchical hydrodynamic flow confinement: efficient use and retrieval of chemicals for microscale chemistry on surfaces

A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control

Delivery of very small amounts of reagents to the near-field of cells with micrometer spatial precision and millisecond time resolution is currently out of reach. Here we present μkiss as a micropipette-based scheme for brushing a layer of small molecules and nanoparticles onto the live cell membrane from a subfemtoliter confined volume of a perfusion flow. We characterize our system through both experiments and modeling, and find excellent agreement. We demonstrate several applications that benefit from a controlled brush delivery, such as a direct means to quantify local and long-range membrane mobility and organization as well as dynamical probing of intercellular force signaling.

The 2D microfluidics cookbook - modeling convection and diffusion in plane flow devices

A growing number of microfluidic systems operate not through networks of microchannels but instead through using 2D flow fields. While the design rules for channel networks are already well-known and exposed in microfluidics textbooks, the knowledge underlying transport in 2D microfluidics remains scattered piecemeal and is not easily accessible to experimentalists and engineers. In this tutorial review, we formulate a unified framework for understanding, analyzing and designing 2D microfluidic technologies. We first show how a large number of seemingly different devices can all be modelled using the same concepts, namely flow and diffusion in a Hele-Shaw cell. We then expose a handful of mathematical tools, accessible to any engineer with undergraduate level mathematics knowledge, namely potential flow, superposition of charges, conformal transforms and basic convection-diffusion. We show how these tools can be combined to obtain a simple "recipe" that models almost any imaginable 2D microfluidic system. We end by pointing to more advanced topics beyond 2D microfluidics, namely interface problems and flow and diffusion in the third dimension. This forms the basis of a complete theory allowing for the design and operation of new microfluidic systems.

Quantifying Antibody Binding Kinetics on Fixed Cells and Tissues via Fluorescence Lifetime Imaging

We present a method for monitoring spatially localized antigen-antibody binding events on physiologically relevant substrates (cell and tissue sections) using fluorescence lifetime imaging. Specifically, we use the difference between the fluorescence decay times of fluorescently tagged antibodies in free solution and in the bound state to track the bound fraction over time and hence deduce the binding kinetics. We make use of a microfluidic probe format to minimize the mass transport effects and localize the analysis to specific regions of interest on the biological substrates. This enables measurement of binding constants (k_on) on surface-bound antigens and on cell blocks using model biomarkers. Finally, we directly measure p53 kinetics with differential biomarker expression in ovarian cancer tissue sections, observing that the degree of expression corresponds to the changes in k_on, with values of 3.27-3.50 × 10³ M^-1 s^-1 for high biomarker expression and 2.27-2.79 × 10³ M^-1 s^-1 for low biomarker expression.

Emerging open microfluidics for cell manipulation

Cell manipulation is the foundation of biochemical studies, which demands user-friendly, multifunctional and precise tools. Based on flow confinement principles, open microfluidics can control the movement of microscale liquid in open space. Every position of the circuit is accessible to external instruments, making it possible to perform precise treatment and analysis of cells at arbitrary target positions especially at the single-cell/sub-cell level. Benefiting from its unique superiority, various manipulations including patterned cell culture, 3D tissue modelling, localized chemical stimulation, online cellular factor analysis, single cell sampling, partial cell treatment, and subcellular free radical attack can be easily realized. In this tutorial review, we summarize two basic ideas to design open microfluidics: open microfluidic networks and probes. The principles of mainstream open microfluidic methods are explained, and their recent important applications are introduced. Challenges and developing trends of open microfluidics are also discussed.

Pixel-based open-space microfluidics for versatile surface processing

An increasing number of applications in biology, chemistry, and material sciences require fluid manipulation beyond what is possible with current automated pipette handlers, such as gradient generation, interface reactions, reagent streaming, and reconfigurability. In this article, we introduce the pixelated chemical display (PCD), a scalable strategy for highly parallel, reconfigurable liquid handling on open surfaces. Microfluidic "pixels" are created when a fluid stream injected above a surface is confined by neighboring identical fluid streams, forming a repeatable flow unit that can be used to tesselate a surface. PCDs generating up to 144 pixels are fabricated and used to project "chemical moving pictures" made of several reagents over both immersed and dry surfaces, without any physical barrier or wall. This work distinguishes itself from previous work in open-space microfluidics by presenting a device architecture where the number of confinement areas can be scaled to any size. Furthermore, it challenges the open-space tenet that the aspiration rate must be higher than the injection rate for reagents to be confined. Overall, this article sets the foundation for massively parallel surface processing using continuous flow streams and showcases possibilities in both wet and dry surface patterning and roll-to-roll processes.

Patterning Biological Gels for 3D Cell Culture inside Microfluidic Devices by Local Surface Modification through Laminar Flow Patterning

Microfluidic devices are used extensively in the development of new in vitro cell culture models like organs-on-chips. A typical feature of such devices is the patterning of biological hydrogels to offer cultured cells and tissues a controlled three-dimensional microenvironment. A key challenge of hydrogel patterning is ensuring geometrical confinement of the gel, which is generally solved by inclusion of micropillars or phaseguides in the channels. Both of these methods often require costly cleanroom fabrication, which needs to be repeated even when only small changes need be made to the gel geometry, and inadvertently expose cultured cells to non-physiological and mechanically stiff structures. Here, we present a technique for facile patterning of hydrogel geometries in microfluidic chips, but without the need for any confining geometry built into the channel. Core to the technique is the use of laminar flow patterning to create a hydrophilic path through an otherwise hydrophobic microfluidic channel. When a liquid hydrogel is injected into the hydrophilic region, it is confined to this path by the surrounding hydrophobic regions. The various surface patterns that are enabled by laminar flow patterning can thereby be rendered into three-dimensional hydrogel structures. We demonstrate that the technique can be used in many different channel geometries while still giving the user control of key geometric parameters of the final hydrogel. Moreover, we show that human umbilical vein endothelial cells can be cultured for multiple days inside the devices with the patterned hydrogels and that they can be stimulated to migrate into the gel under the influence of trans-gel flows. Finally, we demonstrate that the patterned gels can withstand trans-gel flow velocities in excess of physiological interstitial flow velocities without rupturing or detaching. This novel hydrogel-patterning technique addresses fundamental challenges of existing methods for hydrogel patterning inside microfluidic chips, and can therefore be applied to improve design time and the physiological realism of microfluidic cell culture assays and organs-on-chips.

Open Space Diffusive Filter for Simultaneous Species Retrieval and Separation

We present a novel method for the local retrieval of surface bound species and their rapid in-line separation using an open space microfluidic device. Separation can be performed in less than 30 s using the difference in diffusivities within parallel microfluidic flows. As a proof-of-principle, we report the rapid and efficient filtration of polystyrene beads from small molecules and surface bound red blood cells from dimethyl sulfoxide for antigen typing.

Spatially multiplexed RNA in situ hybridization to reveal tumor heterogeneity

Multiplexed RNA in situ hybridization for the analysis of gene expression patterns plays an important role in investigating development and disease. Here, we present a method for multiplexed RNA-ISH to detect spatial tumor heterogeneity in tissue sections. We made use of a microfluidic chip to deliver ISH-probes locally to regions of a few hundred micrometers over time periods of tens of minutes. This spatial multiplexing method can be combined with ISH-approaches based on signal amplification, with bright field detection and with the commonly used format of formalin-fixed paraffin-embedded tissue sections. By using this method, we analyzed the expression of HER2 with internal positive and negative controls (ActB, dapB) as well as predictive biomarker panels (ER, PgR, HER2) in a spatially multiplexed manner on single mammary carcinoma sections. We further demonstrated the applicability of the technique for subtype differentiation in breast cancer. Local analysis of HER2 revealed medium to high spatial heterogeneity of gene expression (Cohen effect size r = 0.4) in equivocally tested tumor tissues. Thereby, we exemplify the importance of using such a complementary approach for the analysis of spatial heterogeneity, in particular for equivocally tested tumor samples. As the method is compatible with a range of ISH approaches and tissue samples, it has the potential to find broad applicability in the context of molecular analysis of human diseases.

Electrokinetic Scanning Probe

The theoretical analysis and experimental demonstration of a new concept are presented for a non-contact scanning probe, in which transport of fluid and molecules is controlled by electric fields. The electrokinetic scanning probe (ESP) enables local chemical and biochemical interactions with surfaces in liquid environments. The physical mechanism and design criteria for such a probe are presented, and its compatibility with a wide range of processing solutions and pH values are demonstrated. The applicability of the probe is shown for surface patterning in conjunction with localized heating and 250-fold analyte stacking.

Microfluidic device fabrication mediated by surface chemical bonding

This review discusses on various bonding techniques for fabricating microdevices with a special emphasis on the modification of surface assisted by the use of chemicals to assemble microfluidic devices at room temperature under atmospheric pressure.

Microfluidic technology for investigation of protein function in single adherent cells

Instrumental techniques and associated methods for single cell analysis, designed to investigate and measure a broad range of cellular parameters in search of unique features, address key limitations of conventional cell-based assays with their ensemble average response. While many different single cell techniques exist for suspension cultures, which can process and characterize large numbers of individual cells in rapid succession, the access to surface-immobilized cells in typical 2D and 3D culture environments remains challenging. Open space microfluidics has created new possibilities in this area, allowing for exclusive access to single cells in adherent cultures, even at high confluency. In this chapter, we briefly review new microtechnologies for the investigation of protein function in single adherent cells, and present an overview over related recent applications of the multifunctional pipette (Biopen), a microfluidic multi-solution dispensing system that uses hydrodynamic confinement in open volume environments in order to establish a superfusion zone over selected single cells in adherent cultures.

Microfluidic multipoles theory and applications

Microfluidic multipoles (MFMs) have been realized experimentally and hold promise for "open-space" biological and chemical surface processing. Whereas convective flow can readily be predicted using hydraulic-electrical analogies, the design of advanced microfluidic multipole is constrained by the lack of simple, accurate models to predict mass transport within them. In this work, we introduce the complete solutions to mass transport in multipolar microfluidics based on the iterative conformal mapping of 2D advection-diffusion around a simple edge into dipoles and multipolar geometries, revealing a rich landscape of transport modes. The models are validated experimentally with a library of 3D printed devices and found in excellent agreement. Following a theory-guided design approach, we further ideate and fabricate two classes of spatiotemporally reconfigurable multipolar devices that are used for processing surfaces with time-varying reagent streams, and to realize a multistep automated immunoassay. Overall, the results set the foundations for exploring, developing, and applying open-space microfluidic multipoles.

Chemical operations on a living single cell by open microfluidics for wound repair studies and organelle transport analysis

We report a laminar flow based approach that is capable of precisely cutting off or treating a portion of a single cell from its remaining portion in its original adherent state.

Single cells are increasingly recognized to be capable of wound repair that is important for our mechanistic understanding of cell biology. The lack of flexible, facile, and friendly subcellular treatment methods has hindered single-cell wound repair studies and organelle transport analyses. Here we report a laminar flow based approach, we call it fluid cell knife (Fluid CK), that is capable of precisely cutting off or treating a portion of a single cell from its remaining portion in its original adherent state. Local operations on portions of a living single cell in its adherent culture state were applied to various types of cells. Temporal wound repair was successfully observed. Moreover, we successfully stained portions of a living single cell to measure the organelle transport speed (mitochondria as a model) inside a cell. This technique opens up new avenues for cellular wound repair and subcellular behavior analyses.

Local surface modification at precise position using a chemical pen

Push-pull cannula system, which was first proposed by Gaddum, has grown to be an important method for the perfusion of brain and region-selective surface treatment. However, reported push-pull cannula systems only concerned on single reagent applications. Microfluidic system was then an exciting tool for multi-reagent treatment on substrate in closed microchannels. Nowadays, it is still a challenge to apply online mixing and reaction for surface pattern in an open environment. Here, we present a novel method using a chemical pen that enables region-selective online chemical reactions for the micro-surface modification/patterning. We utilized this method to fabricate labeling protein array using an online labeling strategy. Moreover, the device was applied for local modification of biomaterials surface by using a three-component reaction at precise position. This tool was the first demonstration of design to perform online reaction of two different reagents on a real solid sample in an open environment. It was demonstrated a useful method for protein array fabrication with online labeled protein.

Rapid micro fluorescence in situ hybridization in tissue sections

This paper describes a micro fluorescence in situ hybridization (μFISH)-based rapid detection of cytogenetic biomarkers on formalin-fixed paraffin embedded (FFPE) tissue sections. We demonstrated this method in the context of detecting human epidermal growth factor 2 (HER2) in breast tissue sections. This method uses a non-contact microfluidic scanning probe (MFP), which localizes FISH probes at the micrometer length-scale to selected cells of the tissue section. The scanning ability of the MFP allows for a versatile implementation of FISH on tissue sections. We demonstrated the use of oligonucleotide FISH probes in ethylene carbonate-based buffer enabling rapid hybridization within <1 min for chromosome enumeration and 10-15 min for assessment of the HER2 status in FFPE sections. We further demonstrated recycling of FISH probes for multiple sequential tests using a defined volume of probes by forming hierarchical hydrodynamic flow confinements. This microscale method is compatible with the standard FISH protocols and with the Instant Quality FISH assay and reduces the FISH probe consumption ∼100-fold and the hybridization time 4-fold, resulting in an assay turnaround time of <3 h. We believe that rapid μFISH has the potential of being used in pathology workflows as a standalone method or in combination with other molecular methods for diagnostic and prognostic analysis of FFPE sections.

Stagnation point flows in analytical chemistry and life sciences

Isolated microfluidic stagnation points – formed within microfluidic interfaces – have come a long way as a tool for characterizing materials, manipulating micro particles, and generating confined flows and localized chemistries.

Micro fluorescence in situ hybridization (μFISH) for spatially multiplexed analysis of a cell monolayer

We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. This μFISH implementation makes use of a non-contact scanning probe technology, namely, a microfluidic probe (MFP) that hydrodynamically shapes nanoliter volumes of liquid on a surface with micrometer resolution. By confining FISH probes at the tip of this microfabricated scanning probe, we locally exposed approximately 1000 selected MCF-7 cells of a monolayer to perform incubation of probes - the rate-limiting step in conventional FISH. This method is compatible with the standard workflow of conventional FISH, allows re-budgeting of the sample for various tests, and results in a ~ 15-fold reduction in probe consumption. The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. We further demonstrated spatially multiplexed μFISH, enabling the use of spectrally equivalent probes for detailed and real-time analysis of a cell monolayer, which paves the way towards rapid and automated multiplexed FISH on standard cytological supports.

Centimeter-Scale Surface Interactions Using Hydrodynamic Flow Confinements

We present a device and method for selective chemical interactions with immersed substrates at the centimeter-scale. Our implementations enable both, sequential and simultaneous delivery of multiple reagents to a substrate, as well as the creation of gradients of reagents on surfaces. The method is based on localizing submicroliter volumes of liquids on an immersed surface with a microfluidic probe (MFP) using a principle termed hydrodynamic flow confinement (HFC). We here show spatially defined, multiplexed surface interactions while benefiting from the probe capabilities such as non-contact scanning operation and convection-enhanced reaction kinetics. Three-layer glass-Si-glass probes were developed to implement slit-aperture and aperture-array designs. Analytical and numerical analysis helped to establish probe designs and operating parameters. Using these probes, we performed immunohistochemical analysis on individual cores of a human breast-cancer tissue microarray. We applied α-p53 antibodies on a 2 mm diameter core within 2.5 min using a slit-aperture probe (HFC dimension: 0.3 mm × 1.2 mm). Further, multiplexed treatment of a tissue core with α-p53 and α-β-actin antibodies was performed using four adjacent HFCs created with an aperture-array probe (HFC dimension: 4 × 0.3 mm × 0.25 mm). The ability of these devices and methods to perform multiplexed assays, present sequentially different liquids on surfaces, and interact with surfaces at the centimeter-scale will likely spur new and efficient surface assays.

Rapid Subtractive Patterning of Live Cell Layers with a Microfluidic Probe

The microfluidic probe (MFP) facilitates performing local chemistry on biological substrates by confining nanoliter volumes of liquids. Using one particular implementation of the MFP, the hierarchical hydrodynamic flow confinement (hHFC), multiple liquids are simultaneously brought in contact with a substrate. Local chemical action and liquid shaping using the hHFC, is exploited to create cell patterns by locally lysing and removing cells. By utilizing the scanning ability of the MFP, user-defined patterns of cell monolayers are created. This protocol enables rapid, real-time and spatially controlled cell patterning, which can allow selective cell-cell and cell-matrix interaction studies.

Selective local lysis and sampling of live cells for nucleic acid analysis using a microfluidic probe

Heterogeneity is inherent to biology, thus it is imperative to realize methods capable of obtaining spatially-resolved genomic and transcriptomic profiles of heterogeneous biological samples. Here, we present a new method for local lysis of live adherent cells for nucleic acid analyses. This method addresses bottlenecks in current approaches, such as dilution of analytes, one-sample-one-test, and incompatibility to adherent cells. We make use of a scanning probe technology - a microfluidic probe - and implement hierarchical hydrodynamic flow confinement (hHFC) to localize multiple biochemicals on a biological substrate in a non-contact, non-destructive manner. hHFC enables rapid recovery of nucleic acids by coupling cell lysis and lysate collection. We locally lysed ~300 cells with chemical systems adapted for DNA or RNA and obtained lysates of ~70 cells/μL for DNA analysis and ~15 cells/μL for mRNA analysis. The lysates were introduced into PCR-based workflows for genomic and transcriptomic analysis. This strategy further enabled selective local lysis of subpopulations in a co-culture of MCF7 and MDA-MB-231 cells, validated by characteristic E-cadherin gene expression in individually extracted cell types. The developed strategy can be applied to study cell-cell, cell-matrix interactions locally, with implications in understanding growth, progression and drug response of a tumor.

Convection-Enhanced Biopatterning with Recirculation of Hydrodynamically Confined Nanoliter Volumes of Reagents

We present a new methodology for efficient and high-quality patterning of biological reagents for surface-based biological assays. The method relies on hydrodynamically confined nanoliter volumes of reagents to interact with the substrate at the micrometer-length scale. We study the interplay between diffusion, advection, and surface chemistry and present the design of a noncontact scanning microfluidic device to efficiently present reagents on surfaces. By leveraging convective flows, recirculation, and mixing of a processing liquid, this device overcomes limitations of existing biopatterning approaches, such as passive diffusion of analytes, uncontrolled wetting, and drying artifacts. We demonstrate the deposition of analytes, showing a 2- to 5-fold increase in deposition rate together with a 10-fold reduction in analyte consumption while ensuring less than 6% variation in pattern homogeneity on a standard biological substrate. In addition, we demonstrate the recirculation of a processing liquid using a microfluidic probe (MFP) in the context of a surface assay for (i) probing 12 independent areas with a single microliter of processing liquid and (ii) processing a 2 mm² surface to create 170 antibody spots of 50 × 100 μm² area using 1.6 μL of liquid. We observe high pattern quality, conservative usage of reagents, micrometer precision of localization and convection-enhanced fast deposition. Such a device and method may facilitate quantitative biological assays and spur the development of the next generation of protein microarrays.

A neutrophil treadmill to decouple spatial and temporal signals during chemotaxis

After more than 50 years of debates, the role of spatial and temporal gradients during cell chemotaxis is still a contentious matter. One major challenge is that when cells move in response to a heterogeneous chemical environment they are exposed to both spatial and temporal concentration changes. Even in the presence of perfectly stable chemical gradients, moving cells experience temporal changes of concentration simply by moving between locations with different chemical concentrations in a heterogeneous environment. Thus, the effects of the spatial and temporal stimuli cannot be dissociated and studied independently, hampering progress towards understanding the mechanisms of cell chemotaxis. Here we employ microfluidic and other engineering tools to build a system that accomplishes a function analogous to a treadmill at the cellular scale, holding a moving cell at a specified, unchanging location in a chemical gradient. Using this system, we decouple the spatial and temporal gradients around moving human neutrophils and find that temporal gradients are necessary for the directional persistence of human neutrophils during chemotaxis. Our results suggest that temporal chemoattractant changes are important during neutrophil migration and should be taken into account when deciphering the signalling pathways of cell chemotaxis.