Frontiers in single cell analysis: multimodal technologies and their clinical perspectives

Dynamic behavior of DNA molecules in microchannels: exploring deflective, elliptical, and spin motions induced by Saffman and Magnus forces

Precise manipulation of individual DNA molecules entering and leaving the channel ports, as well as their smooth passage across the channel, is essential for the detection and screening of DNA molecules using nano-/micro-fluidic technologies. In this paper, by combining single-molecule fluorescence imaging and numerical simulations, the motion states of DNA molecules translocating through a microfluidic channel under the action of the applied electric field are monitored and analyzed in detail. It is found that, under certain conditions of the applied electric field DNA molecules exhibit various motion states, including translation crossing, deflection outflow, reverse outflow, reciprocal movement, and elliptical movement. Simulations indicate that, under the action of Saffman force, DNA molecules can only undergo deflective motion when they experience a velocity gradient in the microchannel flow field; and they can only undergo elliptical motion when their deflective motion is accompanied by a spin motion. In this case, the Magnus force also plays an important role. The detailed study and elucidation of the movement states, dynamic characteristics and mechanisms of DNA molecules such as the deflective and elliptical motions under the actions of Saffman and Magnus forces have helpful implications for the development of related DNA/gene nano-/microfluidic chips, and for the separation, screening and detection of DNA molecules.

A mini review on recent progress of microfluidic systems for antibody development

Objectives

Antibody is specific reagent that be utilized in various field of biomedical research. Monoclonal antibodies are mostly produced using two common techniques namely hybridoma and antibody engineering, which suffer from some limitations such as boring screening procedures, long production time, low efficacy and a degree of automation. To address these limitations, various microfluidics techniques have been developed for the antibody isolation and screening.

Methods

This study specifically investigates nearly recent reports published in peer-reviewed journals indexed in various databases including Web of Science, Scopus, PubMed, Google Scholar, and Science Direct.

Results

In this study, we identified a total of seventy papers from a pool of 130 articles. These papers focus on the application of three major groups of microfluidic platforms, namely valves, microwells, and droplets, in the development of antibodies using hybridoma method and phage display technology. We provide a summary of these applications and also discuss the key findings in this field. Additionally, we illustrate our discussion with several examples to enhance understanding.

Conclusions

Microfluidics has the potential to serve as a valuable tool in streamlining complex laboratory procedures involved in antibody discovery. However, it is important to note that microfluidics is limited to laboratory settings. Further enhancements are needed to address existing challenges and to make microfluidics a reliable, accurate, and cost-effective tool for antibody discovery.

Microfluidic Impedance Cytometry Enabled One-Step Sample Preparation for Efficient Single-Cell Mass Spectrometry

Single-cell mass spectrometry (MS) is significant in biochemical analysis and holds great potential in biomedical applications. Efficient sample preparation like sorting (i.e., separating target cells from the mixed population) and desalting (i.e., moving the cells off non-volatile salt solution) is urgently required in single-cell MS. However, traditional sample preparation methods suffer from complicated operation with various apparatus, or insufficient performance. Herein, a one-step sample preparation strategy by leveraging label-free impedance flow cytometry (IFC) based microfluidics is proposed. Specifically, the IFC framework to characterize and sort single-cells is adopted. Simultaneously with sorting, the target cell is transferred from the local high-salinity buffer to the MS-compatible solution. In this way, one-step sorting and desalting are achieved and the collected cells can be directly fed for MS analysis. A high sorting efficiency (>99%), cancer cell purity (≈87%), and desalting efficiency (>99%), and the whole workflow of impedance-based separation and MS analysis of normal cells (MCF-10A) and cancer cells (MDA-MB-468) are verified. As a standalone sample preparation module, the microfluidic chip is compatible with a variety of MS analysis methods, and envisioned to provide a new paradigm in efficient MS sample preparation, and further in multi-modal (i.e., electrical and metabolic) characterization of single-cells.

Transcribing the enigma: the B chromosome as a territory of uncharted RNAs

B chromosomes are supernumerary elements found in several groups of eukaryotes, including fungi, plants, and animals. Typically, these chromosomes either originate from their hosts through errors in meiosis or interspecifically through horizontal transfer. While many B chromosomes are primarily heterochromatic and possess a low number of coding genes, these additional elements are still capable of transcribing sequences and exerting influence on the expression of host genes. How B chromosomes escape elimination and which impacts can be promoted in the cell always intrigued the cytogeneticists. In pursuit of understanding the behavior and functional impacts of these extra elements, cytogenetic studies meet the advances of molecular biology, incorporating various techniques into investigating B chromosomes from a functional perspective. In this review, we present a timeline of studies investigating B chromosomes and RNAs, highlighting the advances and key findings throughout their history. Additionally, we identified which RNA classes are reported in the B chromosomes and emphasized the necessity for further investigation into new perspectives on the B chromosome functions. In this context, we present a phylogenetic tree that illustrates which branches either report B chromosome presence or have functional RNA studies related to B chromosomes. We propose investigating other unexplored RNA classes and conducting functional analysis in conjunction with cytogenetic studies to enhance our understanding of the B chromosome from an RNA perspective.

Development of a Microfluidic Flow Cytometer with a Uniform Optical Field (Uni-μFCM) Enabling Quantitative Analysis of Single-Cell Proteins and Its Applications in Leukemia Gating, Tumor Classification, and Hierarchy of Cancer Stem Cells

Fast and quantitative estimation of single-cell proteins with various distribution patterns remains a technical challenge. Here, a microfluidic flow cytometer with a uniform optical field (Uni-μFCM) was developed, which enabled the translation of multicolor fluorescence signals of bound antibodies into targeted protein numbers with arbitrary distributions of biological cells. As the core of Uni-μFCM, a uniform optical field for optical excitation and fluorescence detection was realized by adopting a microfabricated metal window to shape the optical beam for excitation, which was modeled and validated by both numerical simulation and experimental characterization. After the validation of Uni-μFCM in single-cell protein quantification by measuring single-cell expressions of three transcriptional factors from four cell lines of variable sizes and origins, Uni-μFCM was applied to (1) quantify membrane and cytoplasmic markers of myeloid and lymphocytic leukocytes to classify cell lines and normal and patient blood samples; (2) measure single-cell expressions of key cytokines affiliated with gene stabilities, differentiating paired oral and colon tumor cell lines with varied malignancies, and (3) quantify single-cell stemming markers of liver tumor cell lines, cell subtypes, and liver patient samples to determine a variety of lineage hierarchy. By quantitatively assessing complex cellular phenotypes, Uni-μFCM substantially expanded the phenotypic space accessible to single-cell applications in leukemia gating, tumor classification, and hierarchy determination of cancer stem cells.

Performance-enhanced clogging-free viscous sheath constriction impedance flow cytometry

As a label-free and high-throughput single cell analysis platform, impedance flow cytometry (IFC) suffers from clogging caused by a narrow microchannel as mechanical constriction (MC). Current sheath constriction (SC) solutions lack systematic evaluation of the performance and proper guidelines for the sheath fluid. Herein, we hypothesize that the viscosity of the non-conductive liquid is the key to the performance of SC, and propose to employ non-conductive viscous sheath flow in SC to unlock the tradeoff between sensitivity and throughput, while ensuring measurement accuracy. By placing MC and SC in series in the same microfluidic chip, we established an evaluation platform to prove the hypothesis. Through modeling analysis and experiments, we confirmed the accuracy (error < 1.60% ± 4.71%) of SC w.r.t. MC, and demonstrated that viscous non-conductive PEG solution achieved an improved sensitivity (7.92×) and signal-to-noise ratio (1.42×) in impedance measurement, with the accuracy maintained and free of clogging. Viscous SC IFC also shows satisfactory ability to distinguish different types of cancer cells and different subtypes of human breast cancer cells. It is envisioned that viscous SC IFC paves the way for IFC to be really usable in practice with clogging-free, accurate, and sensitive performance.

One-Step Fabrication of Droplet Arrays Using a Biomimetic Structural Chip

In the field of one-step efficient preparation of dewetting droplet arrays, the process is hampered by the requirement for low chemical wettability of solid surfaces, which restricts the complete transition of wetting state and its broad prospects in biological applications. Inspired by the physical structure of the lotus leaf, enabling it to promote the change of the infiltration state of an aqueous solution on the surface, we developed a method of one-step fabrication of droplet arrays on the biomimetic structural chip designed in the present work. This greatly reduces the need for chemical modification techniques to achieve low wettability and reduces the reliance on complex and sophisticated surface preparation techniques, thus improving the fabrication efficiency of droplet arrays fully generated on a chip by one-step operation without the need for extra liquid phase or the control of harsh barometric pressure. We also studied the influence of dimensions of the biomimetic structure and the preparation process parameters such as number of smears and speed of smearing on the preparation rate and uniformity of the droplet arrays. The amplification of templating DNA molecules in the droplet arrays prepared in a one-step fabrication way is also performed to verify its application potential for DNA molecular diagnosis.

Recent advances in microfluidics for single-cell functional proteomics

Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.

Convenient tumor 3D spheroid arrays manufacturing via acoustic excited bubbles for in situ drug screening

The quick and convenient fabrication of in vitro tumor spheroids models has been pursued for clinical drug discovery and personalized therapy. Here, uniform three-dimensional (3D) tumor spheroids are quickly constructed by acoustically excited bubble arrays in a microfluidic chip and performed drug response testing in situ. In detail, bubble oscillation excited by acoustic waves induces second radiation force, resulting in the cells rotating and aggregating into tumor spheroids, which obtain controllable sizes ranging from 30 to 300 μm. These spherical tumor models are located in microfluidic networks, where drug solutions with gradient concentrations are generated from 0 to 18 mg mL^-1, so that the cell spheroids response to drugs can be monitored conveniently and efficiently. This one-step tumor spheroids manufacturing method significantly reduces the model construction time to less than 15 s and increases efficiency by eliminating additional transfer processes. These significant advantages of convenience and high-throughput manufacturing make the tumor models promising for use in tumor treatment and point-of-care diagnosis.

Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models

Functional precision medicine is a new, emerging area that can guide cancer treatment by capturing information from direct perturbations of tumor-derived, living cells, such as by drug sensitivity screening. Precision cancer medicine as currently implemented in clinical practice has been driven by genomics, and current molecular tumor boards rely extensively on genomic characterization to advise on therapeutic interventions. However, genomic biomarkers can only guide treatment decisions for a fraction of the patients. In this review we provide an overview of the current state of functional precision medicine, highlight advances for drug-sensitivity screening enabled by cell culture models, and discuss how artificial intelligence (AI) can be coupled to functional precision medicine to guide patient stratification.

Functional Characterization and Phenotyping of Protoplasts on a Microfluidics-Based Flow Cytometry

A better understanding of the phenotypic heterogeneity of protoplasts requires a comprehensive analysis of the morphological and metabolic characteristics of many individual cells. In this study, we developed a microfluidic flow cytometry with fluorescence sensor for functional characterization and phenotyping of protoplasts to allow an unbiased assessment of the influence of environmental factors at the single cell level. First, based on the measurement of intracellular homeostasis of reactive oxygen species (ROS) with a DCFH-DA dye, the effects of various external stress factors such as H₂O₂, temperature, ultraviolet (UV) light, and cadmium ions on intracellular ROS accumulation in Arabidopsis mesophyll protoplasts were quantitatively investigated. Second, a faster and stronger oxidative burst was observed in Petunia protoplasts isolated from white petals than in those isolated from purple petals, demonstrating the photoprotective role of anthocyanins. Third, using mutants with different endogenous auxin, we demonstrated the beneficial effect of auxin during the process of primary cell wall regeneration. Moreover, UV-B irradiation has a similar accelerating effect by increasing the intracellular auxin level, as shown by double fluorescence channels. In summary, our work has revealed previously underappreciated phenotypic variability within a protoplast population and demonstrated the advantages of a microfluidic flow cytometry for assessing the in vivo dynamics of plant metabolic and physiological indices at the single-cell level.