A microfluidic flow cytometer enabling absolute quantification of single-cell intracellular proteins

High throughput cell stiffness measurement via multiplexed impedance sensors

Since physiological and pathological events change the mechanical properties of cells, tools that rapidly quantify such changes at the single-cell level can advance the utility of cell mechanics as a label-free biomarker. We demonstrate the capability to probe the population-level elastic modulus and fluidity of MDA-MB-231 cells at a throughput of up to 50 cell/second within a portable microchip. Our sensing scheme adapts a code multiplexing scheme to implement a distributed network of sensors throughout the microchip, thereby compressing all sensing events into a single electrical output. To validate our approach, we prepared cell samples whose stiffnesses were manipulated with chemical agents. We confirmed the expected effect of the chemicals agreed with the stiffness measurements reported by our microchip. Such a low-cost electronic assay that rapidly measures mechanical properties enables previously infeasible studies to advance the science of mechanobiology.

A Simple and Low-cost Preliminary Quantification of Target Membrane Protein in Single Cells

To study the heterogeneity of target membrane proteins in single cells with cellular integrity, we proposed a simple and low-cost method to obtain the copy number of the membrane proteins. HeLa cells were labeled by FITC affinity bodies specifically targeting HER2 membrane proteins. The immunolabeled HeLa cells were quantified by a laboratory-built laser induced fluorescence detector. A series of fluorescent microspheres with known number of FITC molecules on the surface were used to establish the calibration curve, instead of the standard fluorescent solutions, because the morphology of the microspheres was similar to the cells, and the distribution of FITC on the spheres were similar to the distribution of HER2 on the HeLa. The fluorescence intensity of the cells was converted to the molecule number of HER2 by the calibration curve. A capillary electrophoresis system was used to drive the microspheres and cells through the detection window. The copy number of HER2 in HeLa cells ranged from 4,036 to 1,224,920 ± 100 (2.5-97.5%), and the median of copy numbers were 104,438 ± 100 per cell. This method for measuring low-abundance membrane proteins can be utilized for the initial exploration of proteomics in ordinary laboratories.

A Miniature Modular Fluorescence Flow Cytometry System

Fluorescence flow cytometry is a powerful instrument to distinguish cells or particles labelled with high-specificity fluorophores. However, traditional flow cytometry is complex, bulky, and inconvenient for users to adjust fluorescence channels. In this paper, we present a modular fluorescence flow cytometry (M-FCM) system in which fluorescence channels can be flexibly arranged. Modules for particle focusing and fluorescence detection were developed. After hydrodynamical focusing, the cells were measured in the detection modules, which were integrated with in situ illumination and fluorescence detection. The signal-to-noise ratio of the detection reached to 33.2 dB. The crosstalk among the fluorescence channels was eliminated. The M-FCM system was applied to evaluate cell viability in drug screening, agreeing well with the commercial cytometry. The modular cytometry presents several outstanding features: flexibility in setting fluorescence channels, cost efficiency, compact construction, ease of operation, and the potential to upgrade for multifunctional measurements. The modular cytometry provides a multifunctional platform for various biophysical measurements, e.g., electrical impedance and refractive-index detection. The proposed work paves an innovative avenue for the multivariate analysis of cellular characteristics.

Advances of 3D Cell Co-Culture Technology Based on Microfluidic Chips

Cell co-culture technology aims to study the communication mechanism between cells and to better reveal the interactions and regulatory mechanisms involved in processes such as cell growth, differentiation, apoptosis, and other cellular activities. This is achieved by simulating the complex organismic environment. Such studies are of great significance for understanding the physiological and pathological processes of multicellular organisms. As an emerging cell cultivation technology, 3D cell co-culture technology, based on microfluidic chips, can efficiently, rapidly, and accurately achieve cell co-culture. This is accomplished by leveraging the unique microchannel structures and flow characteristics of microfluidic chips. The technology can simulate the native microenvironment of cell growth, providing a new technical platform for studying intercellular communication. It has been widely used in the research of oncology, immunology, neuroscience, and other fields. In this review, we summarize and provide insights into the design of cell co-culture systems on microfluidic chips, the detection methods employed in co-culture systems, and the applications of these models.

Single-Cell Proteomics by Barcoded Phage-Displayed Screening via an Integrated Microfluidic Chip

Recent advancements in the profiling of proteomes at the single-cell level necessitate the development of quantitative and versatile platforms, particularly for analyzing rare cells like circulating tumor cells (CTCs). In this chapter, we present an integrated microfluidic chip that utilizes magnetic nanoparticles to capture single tumor cells with exceptional efficiency. This chip enables on-chip incubation and facilitates in situ analysis of cell-surface protein expression. By combining phage-based barcoding with next-generation sequencing technology, we successfully monitored changes in the expression of multiple surface markers induced by CTC adherence. This innovative platform holds significant potential for comprehensive screening of multiple surface antigens simultaneously in rare cells, offering single-cell resolution. Consequently, it will contribute valuable insights into biological heterogeneity and human disease.

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.

Integrated Cardiomyocyte-Based Biosensing Platform for Electroporation-Triggered Intracellular Recording in Parallel with Delivery Efficiency Evaluation

Electroporation is a proven technique that can record action potential of cardiomyocytes and serve for biomolecular delivery. To ensure high cell viability, micro-nanodevices cooperating with low-voltage electroporation are frequently utilized in research, and the effectiveness of delivery for intracellular access is typically assessed using an optical imaging approach like flow cytometry. However, the efficiency of in situ biomedical studies is hampered by the intricacy of these analytical approaches. Here, we develop an integrated cardiomyocyte-based biosensing platform to effectively record action potential and evaluate the electroporation quality in terms of viability, delivery efficiency, and mortality. The ITO-MEA device of the platform possesses sensing/stimulating electrodes which combines with the self-developed system to achieve intracellular action potential recording and delivery by electroporation trigger. Moreover, the image acquisition processing system analyzes various parameters effectively to assess delivery performance. Therefore, this platform has the potential for drug delivery therapy and pathology research for cardiology.

Single-cell HER2 quantification via instant signal amplification in microdroplets

Accurate and ultrasensitive evaluation of human epidermal growth factor receptor 2 (HER2) protein is key to early diagnosis and subtype differentiation of breast cancer. Single-cell analyses to reduce ineffective targeted therapies due to breast cancer heterogeneity and improve patient survival remain challenging. Herein, we reported a novel droplet microfluidic combined with an instant cation exchange signal amplification strategy for quantitative analysis of HER2 protein expression on single cells. In the 160 μm droplets produced by a tapered capillary bundle, abundant Immuno-CdS labeled on HER2-positive cells were replaced by Ag ⁺ to obtain Cd²⁺ that stimulated Rhod-5N fluorescence. This uniformly distributed and instantaneous fluorescence amplification strategy in droplets improves sensitivity and reduces signal fluctuation. Using HER2 modified PS microsphere to simulate single cells, we obtained a linear fitting of HER2-modified concentration and fluorescence intensity in microdroplets with the limit detection of 11.372 pg mL^-1. Moreover, the relative standard deviation (RSD) was 4.2-fold lower than the traditional immunofluorescence technique (2.89% vs 12.21%). The HER2 protein on SK-BR-3 cells encapsulated in droplets was subsequently quantified, ranging from 9862.954 pg mL^-1 and 205.26 pg mL^-1, equivalent to 9.795 × 10⁶ and 2.038 × 10⁵ protein molecules. This detection system provides a universal platform for single-cell sensitive quantitative analysis and contributes to the evaluation of HER2-positive tumors.

Development of constrictional microchannels and the recurrent neural network in single-cell protein analysis

Introduction: As the golden approach of single-cell analysis, fluorescent flow cytometry can estimate single-cell proteins with high throughputs, which, however, cannot translate fluorescent intensities into protein numbers. Methods: This study reported a fluorescent flow cytometry based on constrictional microchannels for quantitative measurements of single-cell fluorescent levels and the recurrent neural network for data analysis of fluorescent profiles for high-accuracy cell-type classification. Results: As a demonstration, fluorescent profiles (e.g., FITC labeled β-actin antibody, PE labeled EpCAM antibody and PerCP labeled β-tubulin antibody) of individual A549 and CAL 27 cells were firstly measured and translated into protein numbers of 0.56 ± 0.43 × 10⁴, 1.78 ± 1.0⁶ × 10⁶ and 8.11 ± 4.89 × 10⁴ of A549 cells (n_cell = 10232), and 3.47 ± 2.45 × 10⁴, 2.65 ± 1.19 × 10⁶ and 8.61 ± 5.25 × 10⁴ of CAL 27 cells (n_cell = 16376) based on the equivalent model of the constrictional microchannel. Then, the feedforward neural network was used to process these single-cell protein expressions, producing a classification accuracy of 92.0% for A549 vs. CAL 27 cells. In order to further increase the classification accuracies, as a key subtype of the recurrent neural network, the long short-term memory (LSTM) neural network was adopted to process fluorescent pulses sampled in constrictional microchannels directly, producing a classification accuracy of 95.5% for A549 vs. CAL 27 cells after optimization. Discussion: This fluorescent flow cytometry based on constrictional microchannels and recurrent neural network can function as an enabling tool of single-cell analysis and contribute to the development of quantitative cell biology.

Pulsation Reduction Using Dual Sidewall-Driven Micropumps

Single-cell manipulation in microfluidic channels at the micrometer scale has recently become common. However, the current mainstream method using a syringe pump and a piezoelectric actuator is not suitable for long-term experiments. Some methods incorporate a pump mechanism into a microfluidic channel, but they are not suitable for mass production owing to their complex structures. Here, we propose a sidewall-driven micropump integrated into a microfluidic device as well as a method for reducing the pulsation of flow. This sidewall-driven micropump consists of small chambers lined up on both sides along the main flow path, with a wall separating the flow path and each chamber being deformed by air pressure. The chambers are pressurized to make the peristaltic motion of the wall possible, which generates flow in the main flow path. This pump can be created in a single layer, which allows a simplified structure to be achieved, although pulsation can occur when the pump is used alone. We created two types of chips with two micropumps placed in the flow path and attempted to reduce pulsation by driving them in different phases. The proposed dually driven micropump reduced pulsation when compared with the single pump. This device enables precise particle control and is expected to contribute to less costly and easier cell manipulation experiments.

Demands and technical developments of clinical flow cytometry with emphasis in quantitative, spectral, and imaging capabilities

As the gold-standard method for single-cell analysis, flow cytometry enables high-throughput and multiple-parameter characterization of individual biological cells. This review highlights the demands for clinical flow cytometry in laboratory hematology (e.g., diagnoses of minimal residual disease and various types of leukemia), summarizes state-of-the-art clinical flow cytometers (e.g., FACSLyricTM by Becton Dickinson, DxFLEX by Beckman Coulter), then considers innovative technical improvements in flow cytometry (including quantitative, spectral, and imaging approaches) to address the limitations of clinical flow cytometry in hematology diagnosis. Finally, driven by these clinical demands, future developments in clinical flow cytometry are suggested.

Quantitative flow cytometry leveraging droplet‐based constriction microchannels with high reliability and high sensitivity

This study presented a quantitative flow cytometry leveraging droplet-based constriction microchannels with high reliability and high sensitivity. Droplets encapsulating single cells and even distribution of fluorescein labeled antibodies removed from targeted cells deformed through the constriction microchannel where the excited fluorescent signals were sampled and interpreted into numbers of proteins based on volume equivalence in measurement of droplets and calibration of fluorescence. To improve the detection reliability, a comprehensive analysis and comparison of multiple stripping agents such as proteinase K, guanidine hydrochloride, and urea was conducted. To improve the detection sensitivity, light modulation was used to address electrical noises and quartz microchannels were fabricated to address optical noises. As a demonstration, based on this quantitative flow cytometry of droplet microfluidics, (1) mutant p53 expressions of single cells were quantified as 1.95 ± 0.60 × 10⁵ (n_cell  = 2918 of A431) and 1.30 ± 0.70 × 10⁵ (n_cell  = 3954 of T47D); (2) single-cell expressions of Ras, c-Myc, and β-tubulin were quantified as 1.90 ± 0.59 × 10⁵ , 4.39 ± 1.44 × 10⁵ , and 2.97 ± 0.81 × 10⁵ (n_cell  = 3298 of CAL 27), 1.83 ± 0.58 × 10⁵ , 2.08 ± 0.13 × 10⁶ , and 1.96 ± 0.74 × 10⁵ (n_cell  = 5459 of WSU-HN6). As a microfluidic tool capable of quantitatively estimating single-cell protein expressions, this methodology may provide a new quantitative perspective for the field of flow cytometry.

Microfluidic flow cytometry for blood-based biomarker analysis

Flow cytometry has proven its capability for rapid and quantitative analysis of individual cells and the separation of targeted biological samples from others. The emerging microfluidics technology makes it possible to develop portable microfluidic diagnostic devices for point-of-care testing (POCT) applications. Microfluidic flow cytometry (MFCM), where flow cytometry and microfluidics are combined to achieve similar or even superior functionalities on microfluidic chips, provides a powerful single-cell characterisation and sorting tool for various biological samples. In recent years, researchers have made great progress in the development of the MFCM including focusing, detecting, and sorting subsystems, and its unique capabilities have been demonstrated in various biological applications. Moreover, liquid biopsy using blood can provide various physiological and pathological information. Thus, biomarkers from blood are regarded as meaningful circulating transporters of signal molecules or particles and have great potential to be used as non (or minimally)-invasive diagnostic tools. In this review, we summarise the recent progress of the key subsystems for MFCM and its achievements in blood-based biomarker analysis. Finally, foresight is offered to highlight the research challenges faced by MFCM in expanding into blood-based POCT applications, potentially yielding commercialisation opportunities.

CITEMOXMBD: A flexible single-cell multimodal omics analysis framework to reveal the heterogeneity of immune cells

Simultaneous measurement of multiple modalities in single-cell analysis, represented by CITE-seq, is a promising approach to link transcriptional changes to cellular phenotype and function, requiring new computational methods to define cellular subtypes and states based on multiple data types. Here, we design a flexible single-cell multimodal analysis framework, called CITEMO, to integrate the transcriptome and antibody-derived tags (ADT) data to capture cell heterogeneity from the multi omics perspective. CITEMO uses Principal Component Analysis (PCA) to obtain a low-dimensional representation of the transcriptome and ADT, respectively, and then employs PCA again to integrate these low-dimensional multimodal data for downstream analysis. To investigate the effectiveness of the CITEMO framework, we apply CITEMO to analyse the cell subtypes of Cord Blood Mononuclear Cells (CBMC) samples. Results show that the CITEMO framework can comprehensively analyse single-cell multimodal samples and accurately identify cell subtypes. Besides, we find some specific immune cells that co-express multiple ADT markers. To better describe the co-expression phenomenon, we introduce the co-expression entropy to measure the heterogeneous distribution of the ADT combinations. To further validate the robustness of the CITEMO framework, we analyse Human Bone Marrow Cell (HBMC) samples and identify different states of the same cell type. CITEMO has an excellent performance in identifying cell subtypes and states for multimodal omics data. We suggest that the flexible design idea of CITEMO can be an inspiration for other single-cell multimodal tasks. The complete source code and dataset of the CITEMO framework can be obtained from https://github.com/studentiz/CITEMO.

Phage-Based Profiling of Rare Single Cells Using Nanoparticle-Directed Capture

Advances in single-cell level profiling of the proteome require quantitative and versatile platforms, especially for rare cell analyses such as circulating tumor cell (CTC) profiling. Here we demonstrate an integrated microfluidic chip that uses magnetic nanoparticles to capture single tumor cells with high efficiency, permits on-chip incubation, and facilitates in situ cell-surface protein expression analysis. Combined with phage-based barcoding and next-generation sequencing technology, we were able to monitor changes in the expression of multiple surface markers stimulated in response to CTC adherence. Interestingly, we found fluctuations in the expression of Frizzled2 (FZD2) that reflected the microenvironment of the single cells. This platform has a high potential for in-depth screening of multiple surface antigens simultaneously in rare cells with single-cell resolution, which will provide further insights regarding biological heterogeneity and human disease.

Absolute Quantification of Protein Copy Number in Single Cells With Immunofluorescence Microscopy Calibrated Using Single-Molecule Microarrays

Great strides toward routine single-cell analyses have been made over the last decade, particularly in the field of transcriptomics. For proteomics, amplification is not currently possible and has necessitated the development of ultrasensitive platforms capable of performing such analyses on single cells. These platforms are improving in terms of throughput and multiplexability but still fall short in relation to more established methods such as fluorescence microscopy. However, microscopy methods rely on fluorescence intensity as a proxy for protein abundance and are not currently capable of reporting this in terms of an absolute copy number. Here, a microfluidic implementation of single-molecule microarrays for single-cell analysis is assessed in its ability to calibrate fluorescence microscopy data. We show that the equivalence of measurements of the steady-state distribution of protein abundance to single-molecule microarray data can be exploited to pave the way for absolute quantitation by fluorescence and immunofluorescence microscopy. The methods presented have been developed using GFP but are extendable to other proteins and other biomolecules of interest.

Advances of Single-Cell Protein Analysis

Proteins play a significant role in the key activities of cells. Single-cell protein analysis provides crucial insights in studying cellular heterogeneities. However, the low abundance and enormous complexity of the proteome posit challenges in analyzing protein expressions at the single-cell level. This review summarizes recent advances of various approaches to single-cell protein analysis. We begin by discussing conventional characterization approaches, including fluorescence flow cytometry, mass cytometry, enzyme-linked immunospot assay, and capillary electrophoresis. We then detail the landmark advances of microfluidic approaches for analyzing single-cell protein expressions, including microfluidic fluorescent flow cytometry, droplet-based microfluidics, microwell-based assay (microengraving), microchamber-based assay (barcoding microchips), and single-cell Western blotting, among which the advantages and limitations are compared. Looking forward, we discuss future research opportunities and challenges for multiplexity, analyte, throughput, and sensitivity of the microfluidic approaches, which we believe will prompt the research of single-cell proteins such as the molecular mechanism of cell biology, as well as the clinical applications for tumor treatment and drug development.

Development of microfluidic platform capable of high-throughput absolute quantification of single-cell multiple intracellular proteins from tumor cell lines and patient tumor samples

Quantification of single-cell proteins plays key roles in cell heterogeneity while due to technical limitations absolute numbers of multiple intracellular proteins from large populations of single cells were still missing, leading to compromised results in cell-type classifications. This paper presents a microfluidic platform capable of high-throughput absolute quantification of single-cell multiple types of intracellular proteins where cells stained with fluorescent labelled antibodies are aspirated into the constriction microchannels with excited fluorescent signals detected and translated into numbers of binding sites of targeted proteins based on calibration curves formed by flushing gradient solutions of fluorescent labelled antibodies directly into constriction microchannels. Based on this approach, single-cell numbers of binding sites of β-actin, α-tubulin and β-tubulin from tens of thousands of five representative tumor cell lines were first quantified, reporting cell-type classification rates of 83.0 ± 7.1%. Then single-cell numbers of binding sites of β-actin, biotin and RhoA from thousands of five tumor cell lines with varieties in malignant levels were quantified, reporting cell-type classification rates of 93.7 ± 2.8%. Furthermore, single-cell numbers of binding sites of Ras, c-Myc and p53 from thousands of cells derived from two oral tumor lines of CAL 27, WSU-HN6 and two oral tumor patient samples were quantified, contributing to high classifications of both tumor cell lines (98.6%) and tumor patient samples (83.4%). In conclusion, the developed microfluidic platform was capable of quantifying multiple intracellular proteins from large populations of single cells, and the collected data of protein expressions enabled effective cell-type classifications.

Flow induced particle separation and collection through linear array pillar microfluidics device

Particle filtration and concentration have great significance in a multitude of applications. Physical filters are nearly indispensable in conventional separation processes. Similarly, microfabrication-based physical filters are gaining popularity as size-based particle sorters, separators, and prefiltration structures for microfluidics platforms. The work presented here introduces a linear combination of obstructions to provide size contrast-based particle separation. Polystyrene particles that are captured along the crossflow filters are packed in the direction of the dead-end filters. Separation of polydisperse suspension of 5 μm and 10 μm diameter polystyrene microspheres is attained with capture efficiency for larger particles as 95%. Blood suspension is used for biocharacterization of the device. A flow induced method is used to improve particle capture uniformity in a single microchannel and reduce microgap clogging to about 30%. This concept is extended to obtain semiquantification obtained by comparison of the initial particle concentration to captured-particle occupancy in a microfiltration channel.

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.

Quantification of Low Copy Number Proteins in Single Cells

We have developed an ultrasensitive and highly selective method to quantify low copy number intracellular proteins in a single cell using a low-cost laser-induced fluorescence (LIF) detector and a BV605 fluorescent probe. Active caspase3 proteins in cells were labeled by corresponding antibody-BV605 fluorescent binding, and a cell was injected into a 20 cm × 50 μm i.d. capillary column, followed by in situ lysis and capillary electrophoresis (CE)-LIF analysis. About seven active caspase3 protein molecules in a detection volume of 91 pL could be detected. In our method, cross-bounding proteins other than active caspase3 could be separated and distinguished by differences of retention time. By using Si photodiode assembly as a fluorescent detector instead of PMT, the dynamic range of the LIF is over 4 orders of magnitude. In this experiment, we found that the number of active caspase3 molecules in 98 single Jurkat cells were from 629 to 12171, reflecting significant heterogeneity among the cells although they were from the same batch. For extended application, it could also be applied to quantify other types of low copy number proteins in a single cell as long as the corresponding antibodies are provided. This high-sensitive method could also be a promising tool for earlier cancer diagnosis and related disease pathway research which is relevant to low copy number proteins. In addition, this low-cost system could also be easily expanded to an array system for high-throughput quantitation of low copy proteins in single cells.

Recent advances in single cell manipulation and biochemical analysis on microfluidics

Single cell analysis has become of great interest with unprecedented capabilities for the systematic investigation of cell-to-cell variation in large populations. Rapid and multi-parametric analysis of intercellular biomolecules at the single-cell level is imperative for the improvement of early disease diagnosis and personalized medicine. However, the small size of cells and the low concentration levels of target biomolecules are critical challenges for single cell analysis. In recent years, microfluidic platforms capable of handling small-volume fluid have been demonstrated to be powerful tools for single cell analysis. In addition, microfluidic techniques allow for precise control of the localized microenvironment, which yield more accurate outcomes. Many different microfluidic techniques have been greatly improved for highly efficient single-cell manipulation and highly sensitive detection over the past few decades. To date, microfluidics-based single cell analysis has become the hot research topic in this field. In this review, we particularly highlight the advances in this field during the past three years in the following three aspects: (1) microfluidic single cell manipulation based on microwells, micropatterns, droplets, traps and flow cytometric methods; (2) detection methods based on fluorescence, mass spectrometry, electrochemical, and polymerase chain reaction-based analysis; (3) applications in the fields of small molecule detection, protein analysis, multidrug resistance analysis, and single cell sequencing with droplet microfluidics. We also discuss future research opportunities by focusing on key performances of throughput, multiparametric target detection and data processing.

Cross-Correlative Single-Cell Analysis Reveals Biological Mechanisms of Nanoparticle Radiosensitization

Nanoparticle radiosensitization has been demonstrated well to enhance the effects of radiotherapy, motivate the improvement of therapeutic ratios, and decrease morbidity in cancer treatment. A significant challenge exists in optimizing formulations and translation due to insufficient knowledge of the associated mechanisms, which have historically been limited to physical concepts. Here, we investigated a concept for the role of biological mechanisms. The mere presence of gold nanoparticles led to a down-regulation of thymidylate synthase, important for DNA damage repair in the radioresistant S-phase cells. By developing a cross-correlative methodology to reveal probabilistic gold nanoparticle uptake by cell sub-populations and the associated sensitization as a function of the uptake, a number of revealing observations have been achieved. Surprisingly, for low numbers of nanoparticles, a desensitization action was observed. Sensitization was discovered to preferentially impact S-phase cells, in which impairment of the DNA damage response by the homologous recombination pathway dominates. This small but radioresistant cell population correlates with much greater proliferative ability. Thus, a paradigm is presented whereby enhanced DNA damage is not necessarily due to an increase in the number of DNA double-strand breaks (DSBs) created but can be from a nanoparticle-induced impairment of the damage response by down-regulating repair proteins such as thymidylate synthase.

Single-Cell Omics Analyses Enabled by Microchip Technologies

Single-cell omics studies provide unique information regarding cellular heterogeneity at various levels of the molecular biology central dogma. This knowledge facilitates a deeper understanding of how underlying molecular and architectural changes alter cell behavior, development, and disease processes. The emerging microchip-based tools for single-cell omics analysis are enabling the evaluation of cellular omics with high throughput, improved sensitivity, and reduced cost. We review state-of-the-art microchip platforms for profiling genomics, epigenomics, transcriptomics, proteomics, metabolomics, and multi-omics at single-cell resolution. We also discuss the background of and challenges in the analysis of each molecular layer and integration of multiple levels of omics data, as well as how microchip-based methodologies benefit these fields. Additionally, we examine the advantages and limitations of these approaches. Looking forward, we describe additional challenges and future opportunities that will facilitate the improvement and broad adoption of single-cell omics in life science and medicine.

Microfluidic Analyzer Enabling Quantitative Measurements of Specific Intracellular Proteins at the Single-Cell Level

This paper presents a microfluidic instrument capable of quantifying single-cell specific intracellular proteins, which are composed of three functioning modules and two software platforms. Under the control of a LabVIEW platform, a pressure module flushed cells stained with fluorescent antibodies through a microfluidic module with fluorescent intensities quantified by a fluorescent module and translated into the numbers of specific intracellular proteins at the single-cell level using a MATLAB platform. Detection ranges and resolutions of the analyzer were characterized as 896.78–6.78 × 10⁵ and 334.60 nM for Alexa 488, 314.60–2.11 × 10⁵ and 153.98 nM for FITC, and 77.03–5.24 × 10⁴ and 37.17 nM for FITC-labelled anti-beta-actin antibodies. As a demonstration, the numbers of single-cell beta-actins of two paired oral tumor cell types and two oral patient samples were quantified as: 1.12 ± 0.77 × 10⁶/cell (salivary adenoid cystic carcinoma parental cell line (SACC-83), n_cell = 13,689) vs. 0.90 ± 0.58 × 10⁵/cell (salivary adenoid cystic carcinoma lung metastasis cell line (SACC-LM), n_cell = 15,341); 0.89 ± 0.69 × 10⁶/cell (oral carcinoma cell line (CAL 27), n_cell = 7357) vs. 0.93 ± 0.69 × 10⁶/cell (oral carcinoma lymphatic metastasis cell line (CAL 27-LN2), n_cell = 6276); and 0.86 ± 0.52 × 10⁶/cell (patient I) vs. 0.85 ± 0.58 × 10⁶/cell (patient II). These results (1) validated the developed analyzer with a throughput of 10 cells/s and a processing capability of ~10,000 cells for each cell type, and (2) revealed that as an internal control in cell analysis, the expressions of beta-actins remained stable in oral tumors with different malignant levels.

A Microfluidic Fluorescent Flow Cytometry Capable of Quantifying Cell Sizes and Numbers of Specific Cytosolic Proteins

This study presents a microfluidics based cytometry capable of characterizing cell sizes and counting numbers of specific cytosolic proteins where cells were first bound by antibodies labelled with fluorescence and then aspirated into a constriction microchannel in which fluorescent levels were measured. These raw fluorescent pulses were further divided into a rising domain, a stable domain and a declining domain. In addition, antibody solutions with labelled fluorescence were aspirated through the constriction microchannel, yielding curves to translate raw fluorescent levels to protein concentrations. By using key parameters of three domains as well as the calibration curves, cell diameters and the absolute number of β-actins at the single-cell level were quantified as 14.2 ± 1.7 μm and 9.62 ± 4.29 × 10⁵ (A549, n_cell = 14 242), 13.0 ± 2.0 μm and 6.46 ± 3.34 × 10⁵ (Hep G2, n_cell = 35 932), 13.8 ± 1.9 μm and 1.58 ± 0.90 × 10⁶ (MCF 10 A, n_cell = 16 650), and 12.7 ± 1.5 μm and 1.09 ± 0.49 × 10⁶ (HeLa, n_cell = 26 246). This platform could be further adopted to measure numbers of various cytosolic proteins, providing key insights in proteomics at the single-cell level.

Absolute Copy Numbers of β-Actin Proteins Collected from 10,000 Single Cells

Semi-quantitative studies have located varied expressions of β-actin proteins at the population level, questioning their roles as internal controls in western blots, while the absolute copy numbers of β-actins at the single-cell level are missing. In this study, a polymeric microfluidic flow cytometry was used for single-cell analysis, and the absolute copy numbers of single-cell β-actin proteins were quantified as 9.9 ± 4.6 × 10⁵, 6.8 ± 4.0 × 10⁵ and 11.0 ± 5.5 × 10⁵ per cell for A549 (n_cell = 14,754), Hep G2 (n_cell = 36,949), and HeLa (n_cell = 24,383), respectively. High coefficients of variation (~50%) and high quartile coefficients of dispersion (~30%) were located, indicating significant variations of β-actin proteins within the same cell type. Low p values (≪0.01) and high classification rates based on neural network (~70%) were quantified among A549, Hep G2 and HeLa cells, suggesting expression differences of β-actin proteins among three cell types. In summary, the results reported here indicate significant variations of β-actin proteins within the same cell type from cell to cell, and significant expression differences of β-actin proteins among different cell types, strongly questioning the properties of using β-actin proteins as internal controls in western blots.