Ultrasound-Induced Cell–Cell Interaction Studies in a Multi-Well Microplate

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.

In vitro models to study natural killer cell dynamics in the tumor microenvironment

Immunotherapy is revolutionizing cancer therapy. The rapid development of new immunotherapeutic strategies to treat solid tumors is posing new challenges for preclinical research, demanding novel in vitro methods to test treatments. Such methods should meet specific requirements, such as enabling the evaluation of immune cell responses like cytotoxicity or cytokine release, and infiltration into the tumor microenvironment using cancer models representative of the original disease. They should allow high-throughput and high-content analysis, to evaluate the efficacy of treatments and understand immune-evasion processes to facilitate development of new therapeutic targets. Ideally, they should be suitable for personalized immunotherapy testing, providing information for patient stratification. Consequently, the application of in vitro 3-dimensional (3D) cell culture models, such as tumor spheroids and organoids, is rapidly expanding in the immunotherapeutic field, coupled with the development of novel imaging-based techniques and -omic analysis. In this paper, we review the recent advances in the development of in vitro 3D platforms applied to natural killer (NK) cell-based cancer immunotherapy studies, highlighting the benefits and limitations of the current methods, and discuss new concepts and future directions of the field.

Miniaturized and multiplexed high-content screening of drug and immune sensitivity in a multichambered microwell chip

Here, we present a methodology based on multiplexed fluorescence screening of two- or three-dimensional cell cultures in a newly designed multichambered microwell chip, allowing direct assessment of drug or immune cell cytotoxic efficacy. We establish a framework for cell culture, formation of tumor spheroids, fluorescence labeling, and imaging of fixed or live cells at various magnifications directly in the chip together with data analysis and interpretation. The methodology is demonstrated by drug cytotoxicity screening using ovarian and non-small cell lung cancer cells and by cellular cytotoxicity screening targeting tumor spheroids of renal carcinoma and ovarian carcinoma with natural killer cells from healthy donors. The miniaturized format allowing long-term cell culture, efficient screening, and high-quality imaging of small sample volumes makes this methodology promising for individualized cytotoxicity tests for precision medicine.

Numerical and experimental analysis of a hybrid material acoustophoretic device for manipulation of microparticles

Acoustophoretic microfluidic devices have been developed for accurate, label-free, contactless, and non-invasive manipulation of bioparticles in different biofluids. However, their widespread application is limited due to the need for the use of high quality microchannels made of materials with high specific acoustic impedances relative to the fluid (e.g., silicon or glass with small damping coefficient), manufactured by complex and expensive microfabrication processes. Soft polymers with a lower fabrication cost have been introduced to address the challenges of silicon- or glass-based acoustophoretic microfluidic systems. However, due to their small acoustic impedance, their efficacy for particle manipulation is shown to be limited. Here, we developed a new acoustophoretic microfluid system fabricated by a hybrid sound-hard (aluminum) and sound-soft (polydimethylsiloxane polymer) material. The performance of this hybrid device for manipulation of bead particles and cells was compared to the acoustophoretic devices made of acoustically hard materials. The results show that particles and cells in the hybrid material microchannel travel to a nodal plane with a much smaller energy density than conventional acoustic-hard devices but greater than polymeric microfluidic chips. Against conventional acoustic-hard chips, the nodal line in the hybrid microchannel could be easily tuned to be placed in an off-center position by changing the frequency, effective for particle separation from a host fluid in parallel flow stream models. It is also shown that the hybrid acoustophoretic device deals with smaller temperature rise which is safer for the actuation of bioparticles. This new device eliminates the limitations of each sound-soft and sound-hard materials in terms of cost, adjusting the position of nodal plane, temperature rise, fragility, production cost and disposability, making it desirable for developing the next generation of economically viable acoustophoretic products for ultrasound particle manipulation in bioengineering applications.

Effect of AFM Nanoindentation Loading Rate on the Characterization of Mechanical Properties of Vascular Endothelial Cell

Vascular endothelial cells form a barrier that blocks the delivery of drugs entering into brain tissue for central nervous system disease treatment. The mechanical responses of vascular endothelial cells play a key role in the progress of drugs passing through the blood-brain barrier. Although nanoindentation experiment by using AFM (Atomic Force Microscopy) has been widely used to investigate the mechanical properties of cells, the particular mechanism that determines the mechanical response of vascular endothelial cells is still poorly understood. In order to overcome this limitation, nanoindentation experiments were performed at different loading rates during the ramp stage to investigate the loading rate effect on the characterization of the mechanical properties of bEnd.3 cells (mouse brain endothelial cell line). Inverse finite element analysis was implemented to determine the mechanical properties of bEnd.3 cells. The loading rate effect appears to be more significant in short-term peak force than that in long-term force. A higher loading rate results in a larger value of elastic modulus of bEnd.3 cells, while some mechanical parameters show ambiguous regulation to the variation of indentation rate. This study provides new insights into the mechanical responses of vascular endothelial cells, which is important for a deeper understanding of the cell mechanobiological mechanism in the blood-brain barrier.

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.

Acoustically modulated biomechanical stimulation for human cartilage tissue engineering

Bioacoustofluidics can be used to trap and levitate cells within a fluid channel, thereby facilitating scaffold-free tissue engineering in a 3D environment. In the present study, we have designed and characterised an acoustofluidic bioreactor platform, which applies acoustic forces to mechanically stimulate aggregates of human articular chondrocytes in long-term levitated culture. By varying the acoustic parameters (amplitude, frequency sweep, and sweep repetition rate), cells were stimulated by oscillatory fluid shear stresses, which were dynamically modulated at different sweep repetition rates (1-50 Hz). Furthermore, in combination with appropriate biochemical cues, the acoustic stimulation was tuned to engineer human cartilage constructs with structural and mechanical properties comparable to those of native human cartilage, as assessed by immunohistology and nano-indentation, respectively. The findings of this study demonstrate the capability of acoustofluidics to provide a tuneable biomechanical force for the culture and development of hyaline-like human cartilage constructs in vitro.

Fluorescence activated cell sorting via a focused traveling surface acoustic beam

Fluorescence activated cell sorting (FACS) has become an essential technique widely exploited in biological studies and clinical applications. However, current FACS systems are quite complex, expensive, bulky, and pose potential sample contamination and biosafety issues due to the generation of aerosols in an open environment. Microfluidic technology capable of precise cell manipulation has great potential to reinvent and miniaturize conventional FACS systems. In this work, we demonstrate a benchtop scale FACS system that makes use of a highly focused traveling surface acoustic wave beam to sort out micron-sized particles and biological cells upon fluorescence interrogation at ∼kHz rates. The highly focused acoustic wave beam has a width of ∼50 μm that enables highly accurate sorting of individual particles and cells. We have applied our acoustic FACS system to isolate fluorescently labeled MCF-7 breast cancer cells from diluted whole blood samples with the purity of sorted MCF-7 cells higher than 86%. The cell viability before and after acoustic sorting is higher than 95%, indicating excellent biocompatibility that should enable a variety of cell sorting applications in biomedical research.

Highly focused high-frequency travelling surface acoustic waves (SAW) for rapid single-particle sorting

High-speed sorting is an essential process in a number of clinical and research applications, where single cells, droplets and particles are segregated based on their properties in a continuous flow. With recent developments in the field of microscale actuation, there is increasing interest in replicating the functions available to conventional fluorescence activated cell sorting (FACS) flow cytometry in integrated on-chip systems, which have substantial advantages in cost and portability. Surface acoustic wave (SAW) devices are ideal for many acoustofluidic applications, and have been used to perform such sorting at rates on the order of kHz. Essential to the accuracy of this sorting, however, is the dimensions of the region over which sorting occurs, where a smaller sorting region can largely avoid inaccurate sorting across a range of sample concentrations. Here we demonstrate the use of flow focusing and a highly focused SAW generated by a high-frequency (386 MHz), 10 μm wavelength set of focused interdigital transducers (FIDTs) on a piezoelectric lithium niobate substrate, yielding an effective sorting region only ~25 μm wide, with sub-millisecond pulses generated at up to kHz rates. Furthermore, because of the use of high frequencies, actuation of particles as small as 2 μm can be realized. Such devices represent a substantial step forward in the evolution of highly localized forces for lab-on-a-chip microfluidic applications.

Two-dimensional single-cell patterning with one cell per well driven by surface acoustic waves

In single-cell analysis, cellular activity and parameters are assayed on an individual, rather than population-average basis. Essential to observing the activity of these cells over time is the ability to trap, pattern and retain them, for which previous single-cell-patterning work has principally made use of mechanical methods. While successful as a long-term cell-patterning strategy, these devices remain essentially single use. Here we introduce a new method for the patterning of multiple spatially separated single particles and cells using high-frequency acoustic fields with one cell per acoustic well. We characterize and demonstrate patterning for both a range of particle sizes and the capture and patterning of cells, including human lymphocytes and red blood cells infected by the malarial parasite Plasmodium falciparum. This ability is made possible by a hitherto unexplored regime where the acoustic wavelength is on the same order as the cell dimensions.

Ultrasonic three-dimensional on-chip cell culture for dynamic studies of tumor immune surveillance by natural killer cells

We demonstrate a simple method for three-dimensional (3D) cell culture controlled by ultrasonic standing waves in a multi-well microplate. The method gently arranges cells in a suspension into a single aggregate in each well of the microplate and, by this, nucleates 3D tissue-like cell growth for culture times between two and seven days. The microplate device is compatible with both high-resolution optical microscopy and maintenance in a standard cell incubator. The result is a scaffold- and coating-free method for 3D cell culture that can be used for controlling the cellular architecture, as well as the cellular and molecular composition of the microenvironment in and around the formed cell structures. We demonstrate the parallel production of one hundred synthetic 3D solid tumors comprising up to thousands of human hepatocellular carcinoma (HCC) HepG2 cells, we characterize the tumor structure by high-resolution optical microscopy, and we monitor the functional behavior of natural killer (NK) cells migrating, docking and interacting with the tumor model during culture. Our results show that the method can be used for determining the collective ability of a given number of NK cells to defeat a solid tumor having a certain size, shape and composition. The ultrasound-based method itself is generic and can meet any demand from applications where it is advantageous to monitor cell culture from production to analysis of 3D tissue or tumor models using microscopy in one single microplate device.