One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell.

Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling. Benefiting from the scPMA strategy, we realized dual-omic analysis of single tumor cells, including A549, HeLa, and HepG2 cells with 816, 578, and 293 protein groups and 72, 91, and 148 metabolites quantified on average. A single-cell perspective experiment for investigating the doxorubicin-induced antitumor effects in both the proteome and metabolome aspects was also performed.

Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell.

The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

Simultaneous deep transcriptome and proteome profiling in a single mouse oocyte.

Although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing, and mass spectrometry technology to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19,948 genes and 2,663 protein groups in single mouse oocytes. In particular, we analyzed the correlation of individual RNA and protein pairs, as well as the meiosis regulatory network with unprecedented depth, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, which could be productive for exploring transcriptional and translational regulatory features during oocyte meiosis.

An automated, fully-integrated nucleic acid analyzer based on microfluidic liquid handling robot technique.

On-site nucleic acid testing (NAT) plays an important role for disease monitoring and pathogen diagnosis. In this work, we developed an automated and fully-integrated nucleic acid analyzer by combining the automated liquid handling robot technique with the microfluidic droplet-based real-time PCR assay technique. The present analyzer could achieve multiple operations including sample introduction, nucleic acid extraction based on magnetic solid-phase extraction, reverse transcription and, sample droplet generation, PCR amplification, real-time and dual fluorescence detection of droplet array. A strategy of constructing an integrated compact and low-cost system was adopted to minimize the analyzer size to 50 × 45 × 45 cm (length × width × height), and reduce the instrument cost to ca. $900 with a single analysis cost less than $5. A simple chip was also designed to pre-load reagents and carry oil-covered PCR reaction droplets. We applied the analyzer to identify eight types of influenza pathogens in human throat swabs, and the results were consistent with the colloidal gold method.

Lab at home: a promising prospect for on-site chemical and biological analysis.

The continuing pursuit for a healthy life has led to the urgent need for on-site analysis. In response to the urgent needs of on-site analysis, we propose a novel concept, called lab at home (LAH), for building automated and integrated total analysis systems to perform chemical and biological testing at home. It represents an emerging research area with broad prospects that has not yet attracted sufficient attention. In this paper, we discuss the urgent need, challenges, and future prospects of this area, and the possible roadmap for achieving the goal of LAH has also been proposed.

An integrated microfluidic system for multi-target biochemical analysis of a single drop of blood.

Herein, we described an integrated microfluidic system for multi-target biochemical analysis of micro-volumes of blood samples. This system mainly consists of a microfluid handling module, an integrated microwell array chip, a temperature control module and a spectral detection module. A novel microfluidic plasma extraction approach was developed by coupling the filter membrane-based plasma separation technique with the microfluidic liquid-handling technique. With this approach, quantitative extraction of trace blood with volumes as low as a drop (30 µL) can be automatically realized. Multiple operations in multi-target biochemical analysis are achieved including micro-volume blood collecting, quantitative plasma extraction, plasma dilution, plasma distribution, transferring, biochemical reaction and absorption spectroscopy detection. This system was applied to the multi-target biochemical analysis of glucose, cholesterol and total protein in blood samples and could achieve the determination of the target analytes of a 30-µL blood sample within 11 min. The experimental results are consistent with those obtained by a commercial biochemical analyzer.

An integrated system for automated measurement of airborne pollen based on electrostatic enrichment and image analysis with machine vision.

Here we describe an automated and compact pollen detection system that integrates enrichment, in-situ detection and self-cleaning modules. The system can achieve continuous capture and enrichment of pollen grains in air samples by electrostatic adsorption. The captured pollen grains are imaged with a digital camera, and an automated image analysis based on machine vision is performed, which enables a quantification of the number of pollen particles as well as a preliminary classification into two types of pollen grains. In order to optimize and evaluate the system performance, we developed a testing approach that utilizes an airflow containing a precisely metered amount of pollen particles surrounded by a sheath flow to achieve the generation and lossless transmission of standard gas samples. We studied various factors affecting the pollen capture efficiency, including the applied voltage, air flow rate and humidity. Under optimized conditions, the system was successfully used in the measurement of airborne pollen particles within a wide range of concentrations, spanning 3 orders of magnitude.

LIFGO: A modular laser-induced fluorescence detection system based on plug-in blocks.

In this work, a laser-induced fluorescence (LIF) detection system built in a modular assembling mode was developed based on commercial LEGO blocks and 3D printed blocks. We designed and fabricated a variety of 3D printed building blocks fixed with optical components, including laser light source, filters, lens, dichroic mirror, photodiode detector, and control circuits. Utilizing the relatively high positioning precision of the plug-in blocks, a modular construction strategy was adopted using the flexible plug-in combination of the blocks to build a highly sensitive laser-induced fluorescence detection system, LIFGO. The LIFGO system has a simple structure which could be constructed by inexperienced users within 3 h. We optimized the structure and tested the performance of the LIFGO system, and its detection limits for sodium fluorescein solution in 100 µm i.d. and 250 µm i.d. capillaries were 7 nM and 0.9 nM, respectively. Based on the LIFGO system, we also built a simple capillary electrophoresis (CE) system and applied it to the analysis of DNA fragments to demonstrate its application possibility in biochemical analysis. The separation of 7 fragments in DL500 DNA markers were completed in 600 s. Because of the features of low cost (less than $100) and easy-to-build construction, we introduced the LIFGO system to the experimental teaching of instrumental analysis for undergraduate students. The modular construction form of the LIF detection system greatly reduces the threshold of instrument construction, which is conducive to the popularization of the LIF detection technique in routine laboratories as well as the reform of experimental teaching mode.

Handheld laser-induced fluorescence detection systems with different optical configurations.

There is a growing urgent requirement for miniaturized laser-induced fluorescence (LIF) detection systems in many research fields. In this work, miniaturized LIF detectors with three different optical configurations of orthogonal, confocal, and oblique were developed, using a laser diode as the excitation source and a photodiode as the photodetector. The computer simulation and experimental methods were used to investigate the distributions of laser scattered light and fluorescent light near the detection window. Other conditions including the solution preparation, sample flow rate, alignment method and filter model were also optimized. Under the optimized conditions, the detection limits of sodium fluorescein for orthogonal and confocal LIF detectors were 40 pM and 50 pM, respectively, while the limit of detection (LOD) for oblique LIF detector were 1 nM (45°) and 7 nM (67.5°). We further built a fully integrated handheld orthogonal LIF detector with a total size of 50 × 20 × 46 mm3, a cost of $380, and a detection limit of 10 pM for sodium fluorescein. It is expected that such a LIF detector could be applied in field analysis as a portable instrument or in other analysis systems as a detection module.

A microfluidic robot for rare cell sorting based on machine vision identification and multi-step sorting strategy.

The identification, sorting and analysis of rare target single cells in human blood has always been a clinically meaningful medical challenge. Here, we developed a microfluidic robot platform for sorting specific rare cells from complex clinical blood samples based on machine vision-based image identification, liquid handling robot and droplet-based microfluidic techniques. The robot integrated a cell capture and droplet generation module, a laser-induced fluorescence imaging module, a target cell identification and data analysis module, and a system control module, which could automatically achieve the scanning imaging of cell array, cell identification, capturing, and droplet generation of rare target cells from blood samples containing large numbers of normal cells. Based on the robot platform, a novel "gold panning" multi-step sorting strategy was proposed to achieve the sorting of rare target cells in large-scale cell samples with high operation efficiency and high sorting purity (>90%). The robot platform and the multi-step sorting strategy were applied in the sorting of circulating endothelial progenitor cells (CEPCs) in human blood to demonstrate their feasibility and application potential in the sorting and analysis of rare specific cells. Approximately 1,000 CEPCs were automatically identified from 3,000,000 blood cells at a scanning speed of ca. 4,000 cells/s, and 20 25-nL droplets containing single CEPCs were generated.

A minimalist approach for generating picoliter to nanoliter droplets based on an asymmetrical beveled capillary and its application in digital PCR assay.

We developed a simple approach to form picoliter to nanoliter monodisperse droplets by controlling the interface of an asymmetrical beveled capillary (ABC), with minimalist device of a beveled capillary and a liquid driving module without the need of additional equipment or external forces. We observed an evident leap decrease effect in droplet size specially existed in a capillary with a beveled outlet interface instead of a conventional flat capillary within proper bevel angle and flow rate range, by which droplets with diameters of 2-5 times the inner diameter of the capillary could be spontaneously generated by surface tension. A preliminary theoretical explanation is given to the mechanism of droplet formation at the capillary beveled interface. Various factors affecting the droplet generation process were studied, including capillary hydrophilicity, bevel angle, beveled outlet size, and inner diameter of the capillary, and dispersed phase flow rate. In the optimized condition range, good linear relationship between the droplet volume and the capillary inner diameter (10-100 µm) were obtained, which could be used to conveniently adjust the droplet volume with an adjustable droplet volume range up to 1000 times. Two types of capillaries made of fused silica and polytetrafluoroethylene (PTFE) were adopted for droplet generation using syringe pump, pneumatic pressure or gravity for liquid driving, with the relative standard deviations of droplet volume in the range of 1%-2%. To demonstrate its feasibility, the ABC approach was applied in digital PCR assay for absolute quantification of nucleic acids and identical result as a commercial instrument was obtained. The present approach has features of simple setup, easy to build without needing special microfabrication, low cost, and convenient to use, and could provide a minimalist solution for generating droplets in routine laboratories to perform single molecule analysis, single cell analysis, high-throughput screening, biochemical assays, and chemical synthesis.

Automated microfluidic chip system for radiosynthesis of PET imaging probes.

Positron emission tomography (PET) is a powerful non-invasive molecular imaging technique for the early detection, characterization, and "real-time" monitoring of disease, and for investigating the efficacy of drugs (Phelps, 2000; Ametamey et al., 2008). The development of molecular probes bearing short-lived positron-emitting radionuclides, such as 18F (half-life 110 min) or 11C (half-life 20 min), is crucial for PET imaging to collect in vivo metabolic information in a time-efficient manner (Deng et al., 2019). In this regard, one of the main challenges is rapid synthesis of radiolabeled probes by introducing the radionuclides into pharmaceuticals as soon as possible before injection for a PET scan. Although many potential PET probes have been discovered, only a handful can satisfy the demand for a highly efficient synthesis procedure that achieves radiolabeling and delivery for imaging within 1-2 radioisotope half-lives. Only a few probes, such as 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG) and [18F]fluorodopa, are routinely produced on a commercial scale for daily clinical diagnosis (Grayson et al., 2018; Carollo et al., 2019).

Assembled Step Emulsification Device for Multiplex Droplet Digital Polymerase Chain Reaction.

Digital PCR is a powerful method for absolute nucleic acid quantification with unprecedented accuracy and precision. To promote the wider use and application of digital PCR, several major challenges still exist, including reduction of cost, integration of the instrumental platform, and simplification of operations. This paper describes a reusable microfluidic device that generates nanoliter droplet arrays based on step emulsification for the on-chip multiplex digital PCR of eight samples simultaneously. The device contains two glass plates that can be quickly assembled with prefilled mineral oil. Droplets are simply generated through the arrays of step emulsification nozzles driven by a single pressure controller and are self-assembled into monolayer droplet arrays in U-shaped chambers. The use of mineral oil eliminates bubble generation; thus, no overpressure is required during thermocycling. Moreover, the device can be reused many times after disassembly and a brief cleaning procedure, which significantly reduces the cost of the device per dPCR assays. The device was able to detect template DNA at concentrations as low as 10 copies/µL with a dynamic range of approximately 4 logs. We applied this device in the quantitative assessment of HER2 copy number variation, which is important for targeted therapy and prognosis of breast cancer. The performance was validated by 16 clinical samples, obtaining similar results to commercial digital PCR. We envision that this low-cost, reusable, and user-friendly device can be broadly used in various applications.

A Microfluidic Droplet Array System for Cell-Based Drug Combination Screening.

In the last few decades, drug combination therapy has been widely applied in oncology and in other complex diseases. Due to its potential advantage of lower drug toxicity and higher therapeutic efficacy, drug combination treatment has been more and more studied in fundamental labs and pharmacy companies. In this chapter, we report cell-based drug combination screening using a microfluidic droplet system based on a sequential operation droplet array (SODA) technique. In this system, an oil-covered two-dimensional droplet array chip was used as the platform for cell culture and analysis. This chip was fixed in an x-y-z translation stage under control of a computer program. A tapered capillary connected with a syringe pump was coupled with the droplet array chip to achieve multiple droplet manipulations including liquid metering, aspirating, depositing, mixing, and transferring. Complex multistep operations for drug combination screening involving long-term cell culture, medium changing, schedule-dependent drug dosage and stimulation, and cell viability testing were achieved in parallel using the present system. The drug consumption for each screening test was substantially decreased to 5 ng-5 µg, corresponding to 10- to 1000-fold reductions compared with traditional drug screening systems with 96- or 384-well plates.

A robust and extendable sheath flow interface with minimal dead volume for coupling CE with ESI-MS.

In this paper, we describe a robust sheath flow-based CE-MS interface with minimal interface dead volume based on an extended pattern. A 20µm i.d. × 90µm o.d. fused-silica capillary with a chemically-etched thin-wall tip (30µm o.d.) was used as the separation capillary as well as electrospray emitter, and a 200µm i.d. × 375µm o.d. capillary with a tapered tip (40µm o.d.) was used as the sheath flow capillary. An extendable sheath-flow interface mode was adopted by decreasing the thickness of separation capillary tip and extending the separation capillary tip out from the sheath flow capillary tip, and allowing the sheath flow to be transferred to the separation capillary tip along its outer surface, forming a surface sheath flow to mix with sample flow at the separation capillary tip. Such a strategy could significantly reduce the interface dead volume and thus improve the CE separation efficiency and detection sensitivity, as well as evidently enhance the working reliability of the CE-MS interface. We investigated various factors affecting the interface performance, including capillary extending distance, emitter diameters, sheath flow capillary shape, and sheath flow rate. Under the optimized conditions, a minimal interface dead volume of ca. 4pL was obtained which is the smallest one compared with previously-reported sheath flow-based CE-MS interfaces. The feasibility and applicability of the present CE-MS interface were demonstrated in the separation of a peptide mixture with high separation efficiency of 2.07-3.38µm plate heights and good repeatabilities (< 6.1% RSD, n = 5). We except such a simple and robust interface could provide a possible solution for the development of commercial CE-MS interfaces differing from the currently-used ones, and has the potentials to be applied in routine analytical laboratories for various studies such as proteomics, metabolomics, or single cell analysis.

A Low-Cost Palmtop High-Speed Capillary Electrophoresis Bioanalyzer with Laser Induced Fluorescence Detection.

In this work, we developed a miniaturized palmtop high-speed capillary electrophoresis (CE) system integrating whole modules, including picoliter-scale sample injection, short capillary-based fast CE, high-voltage power supply, orthogonal laser induced fluorescence (LIF) detection, battery, system control, on-line data acquisition, processing, storage, and display modules. A strategy of minimalist miniaturization combining minimal system design and low-cost system construction was adopted to achieve the instrument miniaturization with extremely low cost, which is differing from the current microfabrication strategy used in most reported miniaturized CE systems. With such a strategy, the total size of the bioanalyzer was minimized to 90 × 75 × 77 mm (length × width × height) and the instrument cost was reduced to ca. $500, which demonstrated the smallest and lowest-cost CE instrument with LIF detection in so far reported systems. The present bioanalyzer also exhibited comparable analytical performances to previously-reported high-speed CE systems. A limit of detection of 1.02 nM sodium fluorescein was obtained. Fast separations were achieved for multiple types of samples as amino acids, amino acid enantiomers, DNA fragments, and proteins with high efficiency. We applied this instrument in colorectal cancer diagnosis for detecting KRAS mutation status by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method.

Microdroplet chain array for cell migration assays.

Establishing cell migration assays in multiple different microenvironments is important in the study of tissue repair and regeneration, cancer progression, atherosclerosis, and arthritis. In this work, we developed a miniaturized and massive parallel microfluidic platform for multiple cell migration assays combining the traditional membrane-based cell migration technique and the droplet-based microfluidic technique. Nanoliter-scale droplets are flexibly assembled as building blocks based on a porous membrane to form microdroplet chains with diverse configurations for different assay modes. Multiple operations including in-droplet 2D/3D cell culture, cell co-culture and cell migration induced by a chemoattractant concentration gradient in droplet chains could be flexibly performed with reagent consumption in the nanoliter range for each assay and an assay scale-up to 81 assays in parallel in one microchip. We have applied the present platform to multiple modes of cell migration assays including the accurate cell migration assay, competitive cell migration assay, biomimetic chemotaxis assay, and multifactor cell migration assay based on the organ-on-a-chip concept, for demonstrating its versatility, applicability, and potential in cell migration-related research.

A compact short-capillary based high-speed capillary electrophoresis bioanalyzer.

Here, a compact high-speed CE bioanalyzer based on a short capillary has been developed. Multiple modules of picoliter scale sample injection, high-speed CE separation, sample changing, LIF detection, as well as a custom designed tablet computer for data processing, instrument controlling, and result displaying were integrated in the bioanalyzer with a total size of 23 × 17 × 19 cm (length × width × height). The high-speed CE bioanalyzer is capable of performing automated sample injection and separation for multiple samples and has been successfully applied in fast separations of amino acids, chiral amino acids, proteins and DNA fragments. For instance, baseline separation of six FITC-labeled amino acids and ultrahigh-speed separation of three amino acids could be achieved within 7 and 1 s, respectively. The separation speed and efficiency of the optimized high-speed CE system are comparable to or even better than those reported in microchip-based CE systems. We believe this bioanalyzer could provide an advanced platform for fundamental research in bioscience and clinical diagnosis, as well as in quality control for drugs, foods, and feeds.

A handheld laser-induced fluorescence detector for multiple applications.

In this paper, we present a compact handheld laser-induced fluorescence (LIF) detector based on a 450 nm laser diode and quasi-confocal optical configuration with a total size of 9.1 × 6.2 × 4.1 cm(3). Since there are few reports on the use of 450 nm laser diode in LIF detection, especially in miniaturized LIF detector, we systematically investigated various optical arrangements suitable for the requirements of 450 nm laser diode and system miniaturization, including focusing lens, filter combination, and pinhole, as well as Raman effect of water at 450 nm excitation wavelength. As the result, the handheld LIF detector integrates the light source (450 nm laser diode), optical circuit module (including a 450 nm band-pass filter, a dichroic mirror, a collimating lens, a 525 nm band-pass filter, and a 1.0mm aperture), optical detector (miniaturized photomultiplier tube), as well as electronic module (including signal recording, processing and displaying units). This detector is capable of working independently with a cost of ca. $2000 for the whole instrument. The detection limit of the instrument for sodium fluorescein solution is 0.42 nM (S/N=3). The broad applicability of the present system was demonstrated in capillary electrophoresis separation of fluorescein isothiocyanate (FITC) labeled amino acids and in flow cytometry of tumor cells as an on-line LIF detector, as well as in droplet array chip analysis as a LIF scanner. We expect such a compact LIF detector could be applied in flow analysis systems as an on-line detector, and in field analysis and biosensor analysis as a portable universal LIF detector.

A simple fabrication method for tapered capillary tip and its applications in high-speed CE and ESI-MS.

Fabrication of capillaries with tapered tips is an important technique that is required in many analytical chemistry areas, such as ESI-MS, CE, electrochemical analysis, and microinjection. This paper describes a simple and effective grinding-based fabrication method for capillaries with tapered tips. A novel grinding mode utilizing the combination of rotation and precession of an elastic capillary was developed, which significantly improved the controllability to the grinding process as well as the capillary tip shape. The capillary was fabricated by fixing it in an electric drill installed perpendicularly, and grind the capillary tip rotated around its own axis as well as the drill axis on sandpapers. Compared with conventional fabrication techniques for capillary tips, the present method is easy to control the capillary tip shape in routine laboratories without the requirement of expensive equipments or poisonous reagent (e.g. hydrofluoric acid (HF) solution). Various capillaries with different tip diameters and tip taper angles could be fabricated using the present method with good controllability and reproducibility. These capillaries were applied in high-speed CE and ESI-MS analysis to demonstrate the feasibility and potential of this fabrication method.