A multi-layer microchip for high-throughput single-cell gene expression profiling

Microfluidic Biochips for Single-Cell Isolation and Single-Cell Analysis of Multiomics and Exosomes

Single-cell multiomic and exosome analyses are potent tools in various fields, such as cancer research, immunology, neuroscience, microbiology, and drug development. They facilitate the in-depth exploration of biological systems, providing insights into disease mechanisms and aiding in treatment. Single-cell isolation, which is crucial for single-cell analysis, ensures reliable cell isolation and quality control for further downstream analyses. Microfluidic chips are small lightweight systems that facilitate efficient and high-throughput single-cell isolation and real-time single-cell analysis on- or off-chip. Therefore, most current single-cell isolation and analysis technologies are based on the single-cell microfluidic technology. This review offers comprehensive guidance to researchers across different fields on the selection of appropriate microfluidic chip technologies for single-cell isolation and analysis. This review describes the design principles, separation mechanisms, chip characteristics, and cellular effects of various microfluidic chips available for single-cell isolation. Moreover, this review highlights the implications of using this technology for subsequent analyses, including single-cell multiomic and exosome analyses. Finally, the current challenges and future prospects of microfluidic chip technology are outlined for multiplex single-cell isolation and multiomic and exosome analyses.

Microfluidic Compartmentalization Platforms for Single Cell Analysis

Many cellular analytical technologies measure only the average response from a cell population with an assumption that a clonal population is homogenous. The ensemble measurement often masks the difference among individual cells that can lead to misinterpretation. The advent of microfluidic technology has revolutionized single-cell analysis through precise manipulation of liquid and compartmentalizing single cells in small volumes (pico- to nano-liter). Due to its advantages from miniaturization, microfluidic systems offer an array of capabilities to study genomics, transcriptomics, and proteomics of a large number of individual cells. In this regard, microfluidic systems have emerged as a powerful technology to uncover cellular heterogeneity and expand the depth and breadth of single-cell analysis. This review will focus on recent developments of three microfluidic compartmentalization platforms (microvalve, microwell, and microdroplets) that target single-cell analysis spanning from proteomics to genomics. We also compare and contrast these three microfluidic platforms and discuss their respective advantages and disadvantages in single-cell analysis.

Diameter-definable tubing-microchips for applications in both continuous-flow and TEC-modulated on-chip qPCRs with reaction signal analyzed between different types of Teflon-polymers: PTFE and FEP

Recently, the tubing microfluidic system has attracted significant research interest because it waives complicated microfabrication machineries and bonding procedures during the manufacture of microchips; however, due to the limited dimensions in the market, the commercially available micro-tubes are generally fixed in diameters and are unmodifiable in radius; this makes it a challenge to obtain a randomly defined channel-dimension for a tubing microsystem. To solve this problem, herein, we proposed a novel and simple method to obtain a tubing-channel with gradually changed diameter. Both the tensile forces and spectrophotometric properties have been analyzed in this study for systemic characterization; as a proof-of-concept, the inner diameter (ID) of a fluorinated ethylene propylene (FEP) tube has been modified from 0.5 mm to 0.3 mm, and the FEP tube has been further applied to both the thermoelectric (TEC)-modulated on-chip polymerase chain reactions (PCRs) and the continuous flow on-chip PCRs. To the best of our knowledge, this is the first time that an FEP tube with so small ID has been applied to on-chip qPCRs. Based on the comparison with polytetrafluoroethylene (PTFE) regarding the fluorescence signal inside the tube, it can be verified that FEP has much better detection sensitivity than PTFE although these two materials are reckoned to be belonging to the same type of polymer family, generally referred to as Teflon.

Multi-DNAzymes-functionalized gold nanoparticles for ultrasensitive chemiluminescence detection of thrombin on microchip

Herein, a chemiluminescence assay with dual signal amplification has been developed based on multi-DNAzymes-functionalized gold nanoparticles (AuNPs) using in situ rolling circle amplification (RCA) for ultrasensitive detection of thrombin on microchip. In this assay, AuNPs was functionalized by aptamer and multi-RCA primer for amplification, and thrombin was sandwiched between the aptamer modified on the microchannel and the aptamer linked AuNP. The further amplification was realized by in situ RCA to expand specific oligonucleotides chains on the AuNPs and produce particular multi-DNAzymes. Enhanced chemiluminescence signal was achieved by the catalytic effect of DNAzymes in the luminol-H₂O₂ system. The sensitivity of detection was greatly improved by the dual amplification of multi-RCA primer modified AuNPs, and RCA. The whole strategy was applied for ultrasensitive and specific detection of thrombin. The chemiluminesce assay of thrombin performed a good linear range of 1-25 pM and the limit of detection was as low as 0.55 pM. The successful determination of thrombin in real human serum sample indicated a great potential in clinical study.

A microchip for integrated single-cell genotoxicity assay

With the development of large-scale biologic databases, precision medicine is becoming a frontier in biomedical research. As a main focus of precision medicine study, cancer has been widely accepted as a disease born out of inherited genetic variations or accumulating genomic damage. At the single-cell level, microfluidics or lab-on-a-chip technology for cancer study is an emerging tool for improving risk assessment, diagnostic categories and therapeutic strategies. This work presents a multi-layer microchip for single-cell gene expression profiling. Treated by three drug reagents (i.e. methyl methanesulfonate, docetaxel and colchicine) with varied concentrations and time lengths, individual human breast cancer cells (MCF-7) are then lysed on-chip, and the released mRNA templates are captured and reversely transcribed into cDNA on microbead surface. Three genes (GAPDH, CDKN1A, AURKA) are amplified and quantified simultaneously through triplex real-time polymerase chain reactions (qPCR). Readout per run is set to be eighteen, and can be further improved following same approach. The microchip is able to integrate all steps of single-cell gene expression profiling, and provide precision study of drug induced genotoxicity with reduced reagents consumption per reaction and instrumental cost.

A Microchip for Integrated Single-Cell Gene Expression Profiling and Genotoxicity Detection

Microfluidics-based single-cell study is an emerging approach in personalized treatment or precision medicine studies. Single-cell gene expression holds a potential to provide treatment selections with maximized efficacy to help cancer patients based on a genetic understanding of their disease. This work presents a multi-layer microchip for single-cell multiplexed gene expression profiling and genotoxicity detection. Treated by three drug reagents (i.e., methyl methanesulfonate, docetaxel and colchicine) with varied concentrations and time lengths, individual human cancer cells (MDA-MB-231) are lysed on-chip, and the released mRNA templates are captured and reversely transcribed into single strand DNA. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclin-dependent kinase inhibitor 1A (CDKN1A), and aurora kinase A (AURKA) genes from single cells are amplified and real-time quantified through multiplex polymerase chain reaction. The microchip is capable of integrating all steps of single-cell multiplexed gene expression profiling, and providing precision detection of drug induced genotoxic stress. Throughput has been set to be 18, and can be further increased following the same approach. Numerical simulation of on-chip single cell trapping and heat transfer has been employed to evaluate the chip design and operation.