Acoustofluidics 21: ultrasound-enhanced immunoassays and particle sensors

MultiomicsTracks96: A high throughput PIXUL-Matrix-based toolbox to profile frozen and FFPE tissues multiomes

Background

The multiome is an integrated assembly of distinct classes of molecules and molecular properties, or "omes," measured in the same biospecimen. Freezing and formalin-fixed paraffin-embedding (FFPE) are two common ways to store tissues, and these practices have generated vast biospecimen repositories. However, these biospecimens have been underutilized for multi-omic analysis due to the low throughput of current analytical technologies that impede large-scale studies.

Methods

Tissue sampling, preparation, and downstream analysis were integrated into a 96-well format multi-omics workflow, MultiomicsTracks96. Frozen mouse organs were sampled using the CryoGrid system, and matched FFPE samples were processed using a microtome. The 96-well format sonicator, PIXUL, was adapted to extract DNA, RNA, chromatin, and protein from tissues. The 96-well format analytical platform, Matrix, was used for chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), methylated RNA immunoprecipitation (MeRIP), and RNA reverse transcription (RT) assays followed by qPCR and sequencing. LC-MS/MS was used for protein analysis. The Segway genome segmentation algorithm was used to identify functional genomic regions, and linear regressors based on the multi-omics data were trained to predict protein expression.

Results

MultiomicsTracks96 was used to generate 8-dimensional datasets including RNA-seq measurements of mRNA expression; MeRIP-seq measurements of m6A and m5C; ChIP-seq measurements of H3K27Ac, H3K4m3, and Pol II; MeDIP-seq measurements of 5mC; and LC-MS/MS measurements of proteins. We observed high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles (ChIP-seq: H3K27Ac, H3K4m3, Pol II; MeDIP-seq: 5mC) was able to recapitulate and predict organ-specific super-enhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic expression profiles can be more accurately predicted by the full suite of multi-omics data, compared to using epigenomic, transcriptomic, or epitranscriptomic measurements individually.

Conclusions

The MultiomicsTracks96 workflow is well suited for high dimensional multi-omics studies - for instance, multiorgan animal models of disease, drug toxicities, environmental exposure, and aging as well as large-scale clinical investigations involving the use of biospecimens from existing tissue repositories.

Integrated Acoustic Chip for Culturing 3D Cell Arrays

Three-dimensional (3D) cell arrays provide an in vitro platform for clinical drug screening, but the bulky culture devices limit their application scenarios. Here, we demonstrate an integrated portable device that can realize contact-free construction of 3D cell spheroids. The interaction between the ultrasound generated by the portable device and the capillary results in periodic pressure nodes or anti-nodes, which lead to form a 3D cell array for cell culture. Such a 3D cell array pattern can be constructed in seconds and requires only 1 μL of cell samples. We further assessed the spheroids formed by the portable device and the impact of the acoustic field on spheroids and demonstrated the drug screening with assembled spheroids. More importantly, the integrated acoustic device can be further integrated with other components for more complex cell culture and all-round analysis. This portable and effective integrated device provides a new avenue for clinical biomedicine.

Three-dimensional spiral motion of microparticles by a binary-phase logarithmic-spiral zone plate

Acoustic vortex beams, which have both linear and angular momentum, can be used to make precise acoustic tweezers. Limited by the symmetry of a normal vortex beam, these tweezers are usually used for trapping or rotating particles in two dimensions. Here, the three-dimensional spiral motion of two soft particles of different sizes was realized using a vortex beam with a twisted focus, which was synthesized by a silicone binary-phase logarithmic-spiral zone plate. Numerical simulations and experimental measurements demonstrated that the beam had anisotropic focuses of crescent transverse intensity profiles and a screw phase dislocation with a singularity at the center. Experiments showed that a small particle (k₀r ≈ 1.3) can follow the twisted intensity of the beam, but a large particle (k₀r ≈ 4.7) spirals up away from the twisted field pattern. This is attributed to the dominant gradient force for the small particle, whereas the scattering effect induced a scattering force combined with a gradient force for the large particle. This focused twisted beam, which was generated with a structured silicone plate, and the three-dimensional spiral motion of microparticles, advance the development of simple, compact, and disposable acoustic devices for the precise and diverse manipulation of microparticles.

Wave-Driven Assembly of Quasiperiodic Patterns of Particles

We theoretically show that a superposition of plane waves causes small (compared to the wavelength) particles dispersed in a fluid to assemble in quasiperiodic two or three-dimensional patterns. We experimentally demonstrate this theory by using ultrasound waves to assemble quasiperiodic patterns of carbon nanoparticles in water using an octagonal arrangement of ultrasound transducers, and we document good agreement between theory and experiments. The theory also applies to obtaining quasiperiodic patterns in other situations where particles move with linear waves, such as optical lattices.

Flexural wave-based soft attractor walls for trapping microparticles and cells

Acoustic manipulation of microparticles and cells, called acoustophoresis, inside microfluidic systems has significant potential in biomedical applications. In particular, using acoustic radiation force to push microscopic objects toward the wall surfaces has an important role in enhancing immunoassays, particle sensors, and recently microrobotics. In this paper, we report a flexural-wave based acoustofluidic system for trapping micron-sized particles and cells at the soft wall boundaries. By exciting a standard microscope glass slide (1 mm thick) at its resonance frequencies <200 kHz, we show the wall-trapping action in sub-millimeter-size rectangular and circular cross-sectional channels. For such low-frequency excitation, the acoustic wavelength can range from 10-150 times the microchannel width, enabling a wide design space for choosing the channel width and position on the substrate. Using the system-level acousto-structural simulations, we confirm the acoustophoretic motion of particles near the walls, which is governed by the competing acoustic radiation and streaming forces. Finally, we investigate the performance of the wall-trapping acoustofluidic setup in attracting the motile cells, such as Chlamydomonas reinhardtii microalgae, toward the soft boundaries. Furthermore, the rotation of microalgae at the sidewalls and trap-escape events under pulsed ultrasound are demonstrated. The flexural-wave driven acoustofluidic system described here provides a biocompatible, versatile, and label-free approach to attract particles and cells toward the soft walls.

Periodic particle arrangements using standing acoustic waves

We determine crystal-like materials that can be fabricated by using a standing acoustic wave to arrange small particles in a non-viscous liquid resin, which is cured afterwards to keep the particles in the desired locations. For identical spherical particles with the same physical properties and small compared to the wavelength, the locations where the particles are trapped correspond to the minima of an acoustic radiation potential which describes the net forces that a particle is subject to. We show that the global minima of spatially periodic acoustic radiation potentials can be predicted by the eigenspace of a small real symmetric matrix corresponding to its smallest eigenvalue. We relate symmetries of this eigenspace to particle arrangements composed of points, lines or planes. Since waves are used to generate the particle arrangements, the arrangement's periodicity is limited to certain Bravais lattice classes that we enumerate in two and three dimensions.

Assembling and rotating erythrocyte aggregates by acoustofluidic pressure enabling full phase-contrast tomography

The combined use of ultrasound radiation and microfluidics is a promising tool for aiding the development of lab-on-a-chip devices. In this study, we show that the rotation of linear aggregates of micro-particles can be achieved under the action of acoustic field pressure. This novel manipulation is investigated by tracking polystyrene beads of different sizes through the 3D imaging features of digital holography (DH). From our analysis it is understood that the positioning of the micro-particles and their aggregations are associated with the effect of bulk acoustic radiation forces. The observed rotation is instead found to be compatible with the presence of acoustic streaming patterns as evidenced by our modelling and the resulting numerical simulation. Furthermore, the rotation frequency is shown to depend on the input voltage applied on the acoustic device. Finally, we demonstrate that we can take full advantage of such rotation by combining it with quantitative phase imaging of DH for a significant lab-on-a-chip biomedical application. In fact, we demonstrate that it is possible to put in rotation a linear aggregate of erythrocytes and rely on holographic imaging to achieve a full phase-contrast tomography of the aforementioned aggregate.

Applications of Acoustofluidics in Bioanalytical Chemistry

Acoustics has a broad spectrum of applications, ranging from noise cancelation to ultrasonic imaging. In the past decade, there has been increasing interest in developing acoustic-based methods for biological and biomedical applications. This Perspective summarizes the recent progress in applying acoustofluidic methods (i.e., the fusion of acoustics and microfluidics) to bioanalytical chemistry. We describe the concepts of acoustofluidics and how it can be tailored to different types of bioanalytical applications, including sample concentration, fluorescence-activated cell sorting, label-free cell/particle separation, and fluid manipulation. Examples of each application are given, and the benefits and limitations of these methods are discussed. Finally, our perspectives on the directions that developing solutions should take to address the bottlenecks in the acoustofluidic applications in bioanalytical chemistry are presented.

Ultrasonic Based Tissue Modelling and Engineering

Systems and devices for in vitro tissue modelling and engineering are valuable tools, which combine the strength between the controlled laboratory environment and the complex tissue organization and environment in vivo. Device-based tissue engineering is also a possible avenue for future explant culture in regenerative medicine. The most fundamental requirements on platforms intended for tissue modelling and engineering are their ability to shape and maintain cell aggregates over long-term culture. An emerging technology for tissue shaping and culture is ultrasonic standing wave (USW) particle manipulation, which offers label-free and gentle positioning and aggregation of cells. The pressure nodes defined by the USW, where cells are trapped in most cases, are stable over time and can be both static and dynamic depending on actuation schemes. In this review article, we highlight the potential of USW cell manipulation as a tool for tissue modelling and engineering.

Acoustophoretic separation of infected erythrocytes from blood plasma in a microfluidic platform using biofunctionalized, matched-impedance layers

Acoustophoresis is rapidly gaining prominence in the field of cell manipulation. In recent years, researchers have extensively used this method for separating different types of cells from the bulk fluid. In this paper, we propose a novel acoustophoresis-based technique to capture infected or abnormal erythrocytes from blood plasma. A typical acoustic device consisting of a transducer assembly, microfluidic cavity, and a reflector is considered. Based on the concept of impedance matching, a pair of antibody-coated polystyrene layers is placed in the nodal regions of an acoustic field within the cavity. This technique allows bi-directional migration of the suspended cells to the biofunctionalized surfaces. Therefore, simultaneous capture of infected erythrocytes on both the layers is feasible. Finite element method is used to model the pressure field as well as the motion of erythrocytes under the influence of acoustic radiation, drag, and gravitational forces. A parametric analysis is done by varying the excitation frequency, driving voltage, and the thickness of the polystyrene layers. The resulting changes in the pressure amplitude and field pattern are investigated. The erythrocyte collection efficiency, rate of collection, and the cell distribution on the layer surfaces are also determined under different field conditions. The occurrence of transient cavitation in the blood plasma-filled cavity at the chosen frequency is taken into account by using its threshold pressure value as the limiting factor of pressure amplitude. The study provides an insight into the phenomenon and serves as a guideline to fabricate low-cost, multifunctional rapid diagnostic devices based on acoustophoretic separation.

Acoustic Wave-Driven Functionalized Particles for Aptamer-Based Target Biomolecule Separation

We developed a hybrid microfluidic device that utilized acoustic waves to drive functionalized microparticles inside a continuous flow microchannel and to separate particle-conjugated target proteins from a complex fluid. The acoustofluidic device is composed of an interdigitated transducer that produces high-frequency surface acoustic waves (SAW) and a polydimethylsiloxane (PDMS) microfluidic channel. The SAW interacted with the sample fluid inside the microchannel and deflected particles from their original streamlines to achieve separation. Streptavidin-functionalized polystyrene (PS) microparticles were used to capture aptamer (single-stranded DNA) labeled at one end with a biotin molecule. The free end of the customized aptamer15 (apt15), which was attached to the microparticles via streptavidin-biotin linkage to form the PS-apt15 conjugate, was used to capture the model target protein, thrombin (th), by binding at exosite I to form the PS-apt15-th complex. We demonstrated that the PS-apt15 conjugate selectively captured thrombin molecules in a complex fluid. After the PS-apt15-th complex was formed, the sample fluid was pumped through a PDMS microchannel along with two buffer sheath flows that hydrodynamically focused the sample flow prior to SAW exposure for PS-apt15-th separation from the non-target proteins. We successfully separated thrombin from mCardinal2 and human serum using the proposed acoustofluidic device.

Minimizing antibody cross-reactivity in multiplex detection of biomarkers in paper-based point-of-care assays

Highly multiplexed immunoassays could allow convenient screening of hundreds or thousands of protein biomarkers simultaneously in a clinical sample such as serum or plasma, potentially allowing improved diagnostic accuracy and clinical management of many conditions such as autoimmune disorders, infections, and several cancers. Currently, antibody microarray-based tests are limited in part due to cross reactivity from detection antibody reagents. Here we present a strategy that reduces the cross-reactivity between nanoparticle-bound reporter antibodies through the application of ultrasound energy. By this concept, it was possible to achieve a sensitivity 10(3)-fold (5 pg mL(-1)) lower than when no ultrasound was applied (50 ng mL(-1)) for the simultaneous detection of three different antigens. The detection limits and variability achieved with this technique rival those obtained with other types of multiplex sandwich assays.

Transportation, dispersion and ordering of dense colloidal assemblies by magnetic interfacial rotaphoresis

Colloidal systems exhibit intriguing assembly phenomena with impact in a wide variety of technological fields. The use of magnetically responsive colloids allows one to exploit interactions with an anisotropic dipolar nature. Here, we reveal magnetic interfacial rotaphoresis - a magnetically-induced rotational excitation that imposes a translational motion on colloids by a strong interaction with a solid-liquid interface - as a means to transport, disperse, and order dense colloidal assemblies. By balancing magnetic dipolar and hydrodynamic interactions at a symmetry-breaking interface, rotaphoresis effectuates a translational dispersive motion of the colloids and surprisingly transforms large and dense multilayer assemblies into single-particle layers with quasi-hexagonal ordering within seconds and with velocities of mm s(-1). We demonstrate the application of interfacial rotaphoresis to enhance molecular target capture, showing an increase of the molecular capture rate by more than an order of magnitude.

On-chip ultrasonic sample preparation for cell based assays

We demonstrate pre-alignment, size-based separation, isolation, trapping, up-concentration and fluorescence monitoring of cells in a sequence by the use of a multi-step, three-transducer acoustophoresis chip designed for cellular sample preparation.

Application of an acoustofluidic perfusion bioreactor for cartilage tissue engineering

Cartilage grafts generated using conventional static tissue engineering strategies are characterised by low cell viability, suboptimal hyaline cartilage formation and, critically, inferior mechanical competency, which limit their application for resurfacing articular cartilage defects. To address the limitations of conventional static cartilage bioengineering strategies and generate robust, scaffold-free neocartilage grafts of human articular chondrocytes, the present study utilised custom-built microfluidic perfusion bioreactors with integrated ultrasound standing wave traps. The system employed sweeping acoustic drive frequencies over the range of 890 to 910 kHz and continuous perfusion of the chondrogenic culture medium at a low-shear flow rate to promote the generation of three-dimensional agglomerates of human articular chondrocytes, and enhance cartilage formation by cells of the agglomerates via improved mechanical stimulation and mass transfer rates. Histological examination and assessment of micromechanical properties using indentation-type atomic force microscopy confirmed that the neocartilage grafts were analogous to native hyaline cartilage. Furthermore, in the ex vivo organ culture partial thickness cartilage defect model, implantation of the neocartilage grafts into defects for 16 weeks resulted in the formation of hyaline cartilage-like repair tissue that adhered to the host cartilage and contributed to significant improvements to the tissue architecture within the defects, compared to the empty defects. The study has demonstrated the first successful application of the acoustofluidic perfusion bioreactors to bioengineer scaffold-free neocartilage grafts of human articular chondrocytes that have the potential for subsequent use in second generation autologous chondrocyte implantation procedures for the repair of partial thickness cartilage defects.

Acoustic devices for particle and cell manipulation and sensing

An emerging demand for the precise manipulation of cells and particles for applications in cell biology and analytical chemistry has driven rapid development of ultrasonic manipulation technology. Compared to the other manipulation technologies, such as magnetic tweezing, dielectrophoresis and optical tweezing, ultrasonic manipulation has shown potential in a variety of applications, with its advantages of versatile, inexpensive and easy integration into microfluidic systems, maintenance of cell viability, and generation of sufficient forces to handle particles, cells and their agglomerates. This article briefly reviews current practice and reports our development of various ultrasonic standing wave manipulation devices, including simple devices integrated with high frequency (>20 MHz) ultrasonic transducers for the investigation of biological cells and complex ultrasonic transducer array systems to explore the feasibility of electronically controlled 2-D and 3-D manipulation. Piezoelectric and passive materials, fabrication techniques, characterization methods and possible applications are discussed. The behavior and performance of the devices have been investigated and predicted with computer simulations, and verified experimentally. Issues met during development are highlighted and discussed. To assist long term practical adoption, approaches to low-cost, wafer level batch-production and commercialization potential are also addressed.

Acoustic focusing with engineered node locations for high-performance microfluidic particle separation

We present a new approach to acoustofluidic device design with a secondary channel separated from the main channel by a thin wall. This allows off-center placement of acoustic nodes, which enables high-efficiency and high-throughput separation of cell-scale objects.

Ultrasound assisted particle and cell manipulation on-chip

Ultrasonic fields are able to exert forces on cells and other micron-scale particles, including microbubbles. The technology is compatible with existing lab-on-chip techniques and is complementary to many alternative manipulation approaches due to its ability to handle many cells simultaneously over extended length scales. This paper provides an overview of the physical principles underlying ultrasonic manipulation, discusses the biological effects relevant to its use with cells, and describes emerging applications that are of interest in the field of drug development and delivery on-chip.

Lab-on-a-Chip Magneto-Immunoassays: How to Ensure Contact between Superparamagnetic Beads and the Sensor Surface

Lab-on-a-chip immuno assays utilizing superparamagnetic beads as labels suffer from the fact that the majority of beads pass the sensing area without contacting the sensor surface. Different solutions, employing magnetic forces, ultrasonic standing waves, or hydrodynamic effects have been found over the past decades. The first category uses magnetic forces, created by on-chip conducting lines to attract beads towards the sensor surface. Modifications of the magnetic landscape allow for additional transport and separation of different bead species. The hydrodynamic approach uses changes in the channel geometry to enhance the capture volume. In acoustofluidics, ultrasonic standing waves force µm-sized particles onto a surface through radiation forces. As these approaches have their disadvantages, a new sensor concept that circumvents these problems is suggested. This concept is based on the granular giant magnetoresistance (GMR) effect that can be found in gels containing magnetic nanoparticles. The proposed design could be realized in the shape of paper-based test strips printed with gel-based GMR sensors.

Acoustofluidics 23: acoustic manipulation combined with other force fields

In this, the final paper of the Acoustofluidics series of tutorial articles, we discuss applications in which acoustic radiation forces are used in conjunction with competing or complementary force-fields. This may be in order to enable manipulation operations that would not be easily performed by either force-field alone, or may be used to effect separation based on the different physical principals underlying competing fields. Examples are given of a number of different applications in which acoustic forces are combined with gravitational fields, hydrodynamic forces, electric fields (including dielectrophoresis), magnetic forces and optical forces.

Acoustofluidics 20: applications in acoustic trapping

This part of the Acoustofluidics tutorial series reviews applications in acoustic trapping of micron-sized particles and cells in microfluidic systems. Acoustic trapping enables non-invasive and non-contact immobilisation of cells and particles in microfluidic systems. Acoustic trapping has been used for reducing the time needed to create 3D cell clusters, enhance particle-based bioassays and facilitated interaction studies of both cells and particles. An area that is increasingly interesting is the use of acoustic trapping for enriching low concentration samples and the washing or fractioning of cell populations prior to sensitive detection methods (MALDI-MS, PCR etc.) The main focus of the review is systems where particles can be retained against a flow while applications in which particles are positioned in a stationary fluid will be addressed in part 21 of the Acoustofluidics tutorial series (M. Wiklund, S. Radel and J. J. Hawkes, Lab Chip, 2012, 12, ).