Microfluidics towards single cell resolution protein analysis

Abstract Single cell analysis has aroused great interest with its remarkable ability to investigate cell-to-cell heterogeneity in large populations. However, probing protein information at single cells resolution including quantity, interactions, and dynamics have been great challenges as a result of the small size of cells, the complexity and a large concentration range of the protein and the lack of genome-wide amplification method. Fortunately, microfluidics capable of high throughput, high reproducibility, large parallelization, easy operability and low-cost, has been emerging as a powerful platform for the analysis of single cell proteins. In this review, we focus the recent advances of microfluidics in single cell resolution protein analysis, particularly covering the following aspects: (1) microfluidic electrophoresis (capillary electrophoresis and gel electrophoresis); (2) microfluidic cytometry (microfluidic flow cytometry, droplet based cytometry and image cytometry); (3) microfluidic array (micro wells, micro chambers, valve-based microfluidics and static droplet array microfluidics); (4) microfluidic probe and (5) microfluidics based mass spectrometry.

[1]  Huizeng Li,et al.  Splitting a droplet for femtoliter liquid patterns and single cell isolation. , 2015, ACS applied materials & interfaces.

[2]  Qiushui Chen,et al.  Biochemical analysis on microfluidic chips , 2016 .

[3]  Moran Bercovici,et al.  Rapid phenotypic antimicrobial susceptibility testing using nanoliter arrays , 2017, Proceedings of the National Academy of Sciences.

[4]  Zeper Abliz,et al.  Combination of Droplet Extraction and Pico-ESI-MS Allows the Identification of Metabolites from Single Cancer Cells. , 2018, Analytical chemistry.

[5]  Bifeng Liu,et al.  “Click” chemistry‐based surface modification of poly(dimethylsiloxane) for protein separation in a microfluidic chip , 2010, Electrophoresis.

[6]  Yifan Liu,et al.  Advancing single-cell proteomics and metabolomics with microfluidic technologies. , 2019, The Analyst.

[7]  L. Qin,et al.  Microfluidics Cell Loading‐Dock System: Ordered Cellular Array for Dynamic Lymphocyte‐Communication Study , 2017, Advanced biosystems.

[8]  Thanh D Do,et al.  Categorizing Cells on the Basis of their Chemical Profiles: Progress in Single-Cell Mass Spectrometry , 2017, Journal of the American Chemical Society.

[9]  Hong Wu,et al.  A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens. , 2010, Cancer research.

[10]  Wilhelm T S Huck,et al.  Probing cellular heterogeneity in cytokine-secreting immune cells using droplet-based microfluidics. , 2013, Lab on a chip.

[11]  Yuan-Jie Fan,et al.  Multicolor Fluorescence Detection-Based Microfluidic Device for Single-Cell Metabolomics: Simultaneous Quantitation of Multiple Small Molecules in Primary Liver Cells. , 2016, Analytical chemistry.

[12]  Jun Wang,et al.  Highly Multiplexed Single‐Cell Protein Profiling with Large‐Scale Convertible DNA‐Antibody Barcoded Arrays , 2018, Advanced science.

[13]  Mohammad A. Qasaimeh,et al.  Microfluidic probes for use in life sciences and medicine. , 2013, Lab on a chip.

[14]  Hongkai Wu,et al.  Current Advances in Highly Multiplexed Antibody-Based Single-Cell Proteomic Measurements. , 2017, Chemistry, an Asian journal.

[15]  J Christopher Love,et al.  Immuno-hybridization chain reaction for enhancing detection of individual cytokine-secreting human peripheral mononuclear cells. , 2011, Analytical chemistry.

[16]  Ronald J. Moore,et al.  Proteome Profiling of 1 to 5 Spiked Circulating Tumor Cells Isolated from Whole Blood Using Immunodensity Enrichment, Laser Capture Microdissection, Nanodroplet Sample Processing, and Ultrasensitive nanoLC-MS. , 2018, Analytical chemistry.

[17]  J. Christopher Love,et al.  Nanowell-Based Immunoassays for Measuring Single-Cell Secretion: Characterization of Transport and Surface Binding , 2014, Analytical chemistry.

[18]  Jongyoon Han,et al.  Single Cell Analysis of Leukocyte Protease Activity Using Integrated Continuous-Flow Microfluidics. , 2016, Analytical chemistry.

[19]  Jin‐Ming Lin,et al.  Multi-channel cell co-culture for drug development based on glass microfluidic chip-mass spectrometry coupled platform. , 2016, Rapid communications in mass spectrometry : RCM.

[20]  D. Walt,et al.  Highly Sensitive and Multiplexed Protein Measurements. , 2018, Chemical reviews.

[21]  Bo Huang,et al.  Counting Low-Copy Number Proteins in a Single Cell , 2007, Science.

[22]  Feng Jin,et al.  Recent advances in single cell manipulation and biochemical analysis on microfluidics. , 2019, The Analyst.

[23]  Chang Lu,et al.  Total internal reflection fluorescence flow cytometry. , 2008, Analytical chemistry.

[24]  Amy E Herr,et al.  Fully integrated microfluidic platform enabling automated phosphoprofiling of macrophage response. , 2009, Analytical chemistry.

[25]  C. Ormandy,et al.  Static droplet array for culturing single live adherent cells in an isolated chemical microenvironment. , 2018, Lab on a chip.

[26]  Rong Fan,et al.  Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells , 2011, Proceedings of the National Academy of Sciences.

[27]  Emmanuel Delamarche,et al.  Microfluidics in the "open space" for performing localized chemistry on biological interfaces. , 2012, Angewandte Chemie.

[28]  Thomas D. Perroud,et al.  Microfluidically-unified cell culture, sample preparation, imaging and flow cytometry for measurement of cell signaling pathways with single cell resolution. , 2012, Lab on a chip.

[29]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

[30]  U. Landegren,et al.  Protein detection using proximity-dependent DNA ligation assays , 2002, Nature Biotechnology.

[31]  Ronald J. Moore,et al.  Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells , 2018, Nature Communications.

[32]  Michael J. T. Stubbington,et al.  The Human Cell Atlas: from vision to reality , 2017, Nature.

[33]  Francoise Remacle,et al.  Hypoxia induces a phase transition within a kinase signaling network in cancer cells , 2013, Proceedings of the National Academy of Sciences.

[34]  R. Aebersold,et al.  Mass Spectrometry and Protein Analysis , 2006, Science.

[35]  D. Walt,et al.  Single-Molecule Arrays for Protein and Nucleic Acid Analysis. , 2017, Annual review of analytical chemistry.

[36]  Jun Wang,et al.  Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions , 2014, Proceedings of the National Academy of Sciences.

[37]  N. Allbritton,et al.  Automated capillary electrophoresis system for fast single-cell analysis. , 2013, Analytical chemistry.

[38]  Joo H. Kang,et al.  Stationary nanoliter droplet array with a substrate of choice for single adherent/nonadherent cell incubation and analysis , 2014, Proceedings of the National Academy of Sciences.

[39]  N. Munce,et al.  Microfabricated system for parallel single-cell capillary electrophoresis. , 2004, Analytical chemistry.

[40]  Christopher S. Hughes,et al.  Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes , 2016, Molecular & Cellular Proteomics.

[41]  Amy E Herr,et al.  Profiling protein expression in circulating tumour cells using microfluidic western blotting , 2017, Nature Communications.

[42]  Paul S Mischel,et al.  Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma. , 2016, Cancer cell.

[43]  Xiangmin Zhang,et al.  Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis. , 2015, Analytical chemistry.

[44]  Yu Wu,et al.  High-throughput secretomic analysis of single cells to assess functional cellular heterogeneity. , 2013, Analytical chemistry.

[45]  Wei Wei,et al.  Microchip-based single-cell functional proteomics for biomedical applications. , 2017, Lab on a chip.

[46]  Bifeng Liu,et al.  Environmentally friendly surface modification of PDMS using PEG polymer brush , 2009, Electrophoresis.

[47]  Jin-Ming Lin,et al.  Characterization of drug permeability in Caco-2 monolayers by mass spectrometry on a membrane-based microfluidic device. , 2013, Lab on a chip.

[48]  Y. Zhan,et al.  Kinetics of NF-κB nucleocytoplasmic transport probed by single-cell screening without imaging. , 2010, Lab on a chip.

[49]  Junbo Wang,et al.  A microfluidic flow cytometer enabling absolute quantification of single-cell intracellular proteins. , 2017, Lab on a chip.

[50]  Ronald J. Moore,et al.  Proteomic Analysis of Single Mammalian Cells Enabled by Microfluidic Nanodroplet Sample Preparation and Ultrasensitive NanoLC-MS. , 2018, Angewandte Chemie.

[51]  Ling Lin,et al.  Micro/nanofluidics-enabled single-cell biochemical analysis , 2018 .

[52]  Timothy K Lee,et al.  Single-cell NF-κB dynamics reveal digital activation and analogue information processing , 2010, Nature.

[53]  Utkan Demirci,et al.  Rapid Assembly of Heterogeneous 3D Cell Microenvironments in a Microgel Array , 2016, Advanced materials.

[54]  S. Quake,et al.  A microfabricated fluorescence-activated cell sorter , 1999, Nature Biotechnology.

[55]  D. Lauffenburger,et al.  Microfluidic Probe for Single-Cell Lysis and Analysis in Adherent Tissue Culture , 2014, Nature Communications.

[56]  D. Pe’er,et al.  Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands , 2015, Proceedings of the National Academy of Sciences.

[57]  David Juncker,et al.  Multipurpose microfluidic probe , 2005, Nature materials.

[58]  Y. Yao,et al.  Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform , 2018, Nature Communications.

[59]  E. Verpoorte,et al.  A decade of microfluidic analysis coupled with electrospray mass spectrometry: an overview. , 2007, Lab on a chip.

[60]  A. Regev,et al.  Scaling single-cell genomics from phenomenology to mechanism , 2017, Nature.

[61]  Rong Fan,et al.  Protein signaling networks from single cell fluctuations and information theory profiling. , 2011, Biophysical journal.

[62]  Steve C. C. Shih,et al.  A droplet-to-digital (D2D) microfluidic device for single cell assays. , 2015, Lab on a chip.

[63]  J Christopher Love,et al.  Cellular barcodes for efficiently profiling single-cell secretory responses by microengraving. , 2012, Analytical chemistry.

[64]  A. Abate,et al.  High-throughput injection with microfluidics using picoinjectors , 2010, Proceedings of the National Academy of Sciences.

[65]  Lloyd M Smith,et al.  Integrated microfluidic device for automated single cell analysis using electrophoretic separation and electrospray ionization mass spectrometry. , 2010, Analytical chemistry.

[66]  N. Murthy,et al.  Hydrogel Pore‐Size Modulation for Enhanced Single‐Cell Western Blotting , 2016, Advanced materials.

[67]  Min Huang,et al.  Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis. , 2018, Analytical chemistry.

[68]  Peggy P Y Chan,et al.  Microparticle Delivery of Protein Markers for Single-Cell Western Blotting from Microwells. , 2018, Small.

[69]  Amy E. Herr,et al.  Single-cell western blotting , 2014, Nature Methods.

[70]  Ryan A. Kellogg,et al.  Noise Facilitates Transcriptional Control under Dynamic Inputs , 2015, Cell.

[71]  R Puers,et al.  Digital microfluidics for time-resolved cytotoxicity studies on single non-adherent yeast cells. , 2015, Lab on a chip.

[72]  Renjie Liao,et al.  Highly Multiplexed Single-Cell In Situ Protein Analysis with Cleavable Fluorescent Antibodies. , 2017, Angewandte Chemie.

[73]  X. Zhang,et al.  Design of five‐layer gold nanoparticles self‐assembled in a liquid open tubular column for ultrasensitive nano‐LC‐MS/MS proteomic analysis of 80 living cells , 2017, Proteomics.

[74]  Peter Nemes,et al.  Single‐Cell Mass Spectrometry for Discovery Proteomics: Quantifying Translational Cell Heterogeneity in the 16‐Cell Frog (Xenopus) Embryo , 2016, Angewandte Chemie.

[75]  David S Lawrence,et al.  An Integrated Chemical Cytometry Method: Shining a Light on Akt Activity in Single Cells. , 2016, Angewandte Chemie.

[76]  Garry P Nolan,et al.  Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling , 2006, Nature Methods.

[77]  Chang Lu,et al.  Quantitative analysis of protein translocations by microfluidic total internal reflection fluorescence flow cytometry. , 2010, Lab on a chip.

[78]  Jonathan J. Chen,et al.  A microchip platform for interrogating tumor-macrophage paracrine signaling at the single-cell level. , 2014, Lab on a chip.

[79]  Haifang Li,et al.  In Situ Scatheless Cell Detachment Reveals Correlation between Adhesion Strength and Viability at Single-Cell Resolution. , 2018, Angewandte Chemie.

[80]  Hakho Lee,et al.  Photocleavable DNA barcode-antibody conjugates allow sensitive and multiplexed protein analysis in single cells. , 2012, Journal of the American Chemical Society.

[81]  A. Herr,et al.  Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. , 2016, Angewandte Chemie.

[82]  Paul D Piehowski,et al.  New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells. , 2019, The Analyst.

[83]  Paul J. Choi,et al.  Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells , 2010, Science.

[84]  Martin Lundberg,et al.  Homogeneous antibody-based proximity extension assays provide sensitive and specific detection of low-abundant proteins in human blood , 2011, Nucleic acids research.

[85]  Ruedi Aebersold,et al.  Mass-spectrometric exploration of proteome structure and function , 2016, Nature.

[86]  Lung-Ming Fu,et al.  Review and perspectives on microfluidic flow cytometers , 2018, Sensors and Actuators B: Chemical.

[87]  J. C. Love,et al.  Profiling antibody responses by multiparametric analysis of primary B cells , 2008, Proceedings of the National Academy of Sciences.

[88]  Q. Fang,et al.  Manipulating Femtoliter to Picoliter Droplets by Pins for Single Cell Analysis and Quantitative Biological Assay. , 2018, Analytical chemistry.

[89]  Jianjun Li,et al.  Advances in coupling microfluidic chips to mass spectrometry. , 2015, Mass spectrometry reviews.

[90]  Qiang Zhang,et al.  Recent advances in the use of microfluidic technologies for single cell analysis. , 2017, The Analyst.

[91]  A. Hoffmann,et al.  High-Content Quantification of Single-Cell Immune Dynamics , 2016, Cell reports.

[92]  Tzu-Chiao Chao,et al.  Microfluidic devices for high‐throughput proteome analyses , 2013, Proteomics.

[93]  Ralph Weissleder,et al.  Cancer Cell Profiling by Barcoding Allows Multiplexed Protein Analysis in Fine-Needle Aspirates , 2014, Science Translational Medicine.

[94]  R. Zengerle,et al.  Proximity Ligation Assay for High-content Profiling of Cell Signaling Pathways on a Microfluidic Chip* , 2013, Molecular & Cellular Proteomics.

[95]  S. Quake,et al.  Versatile, fully automated, microfluidic cell culture system. , 2007, Analytical chemistry.

[96]  Fabian J Theis,et al.  The Human Cell Atlas , 2017, bioRxiv.

[97]  Haifang Li,et al.  Adhesion analysis of single circulating tumor cells on a base layer of endothelial cells using open microfluidics† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c8sc03027h , 2018, Chemical science.

[98]  Ling Xu,et al.  Single-cell codetection of metabolic activity, intracellular functional proteins, and genetic mutations from rare circulating tumor cells. , 2015, Analytical chemistry.

[99]  Hsian-Rong Tseng,et al.  Microfluidic image cytometry for quantitative single-cell profiling of human pluripotent stem cells in chemically defined conditions. , 2010, Lab on a chip.

[100]  Kemin Wang,et al.  Proximity-dependent protein detection based on enzyme-assisted fluorescence signal amplification. , 2014, Biosensors & bioelectronics.

[101]  A. Wu,et al.  Development and preliminary clinical validation of a high sensitivity assay for cardiac troponin using a capillary flow (single molecule) fluorescence detector. , 2006, Clinical chemistry.

[102]  Fei Xu,et al.  Single Cell Chemical Proteomics with Membrane-Permeable Activity-Based Probe for Identification of Functional Proteins in Lysosome of Tumors. , 2016, Analytical chemistry.

[103]  Roland Zengerle,et al.  Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip. , 2015, Lab on a chip.

[104]  D. Weitz,et al.  Single-cell analysis and sorting using droplet-based microfluidics , 2013, Nature Protocols.

[105]  R. Zare,et al.  Chemical cytometry on a picoliter-scale integrated microfluidic chip. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[106]  Hiroyuki Fujita,et al.  Microfabricated arrays of femtoliter chambers allow single molecule enzymology , 2005, Nature Biotechnology.

[107]  Nataly Kravchenko-Balasha,et al.  Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement , 2016, Proceedings of the National Academy of Sciences.

[108]  Rong Fan,et al.  Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research , 2013, Genome Medicine.

[109]  Mustafa Khammash,et al.  Digital Quantification of Proteins and mRNA in Single Mammalian Cells. , 2016, Molecular cell.

[110]  K. Jensen,et al.  Live-cell protein labelling with nanometre precision by cell squeezing , 2016, Nature Communications.

[111]  Alar Ainla,et al.  Hydrodynamic Flow Confinement Technology in Microfluidic Perfusion Devices , 2012, Micromachines.

[112]  Rong Fan,et al.  A Clinical Microchip for Evaluation of Single Immune Cells Reveals High Functional Heterogeneity in Phenotypically Similar T Cells Nih Public Access Author Manuscript Design Rationale and Detection Limit of the Scbc Online Methods Microchip Fabrication On-chip Secretion Profiling Supplementary Mater , 2022 .

[113]  David A. Weitz,et al.  Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices , 2017, Nature Reviews Genetics.

[114]  Man He,et al.  Chip-based monolithic microextraction combined with ICP-MS for the determination of bismuth in HepG2 cells , 2016 .

[115]  Bifeng Liu,et al.  Single-cell chemical proteomics with an activity-based probe: identification of low-copy membrane proteins on primary neurons. , 2014, Angewandte Chemie.

[116]  Jin‐Ming Lin,et al.  In Situ Partial Treatment of Single Cells by Laminar Flow in the "Open Space". , 2019, Analytical chemistry.

[117]  Michele Zagnoni,et al.  Intracellular protein determination using droplet-based immunoassays. , 2011, Analytical chemistry.

[118]  Tanyu Wang,et al.  Ultrasensitive microfluidic solid-phase ELISA using an actuatable microwell-patterned PDMS chip. , 2013, Lab on a chip.

[119]  D. Baker,et al.  Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase , 2016, Nature Chemistry.

[120]  Jonathan J. Chen,et al.  Single-Cell Protein Secretion Detection and Profiling. , 2019, Annual review of analytical chemistry.

[121]  Andreas Schmid,et al.  Chemical and biological single cell analysis. , 2010, Current opinion in biotechnology.

[122]  Philippe Nizard,et al.  Microfluidics as a Strategic Player to Decipher Single-Cell Omics? , 2017, Trends in biotechnology.

[123]  Jin‐Ming Lin,et al.  Cell analysis on chip-mass spectrometry , 2018, TrAC Trends in Analytical Chemistry.

[124]  D. Juncker,et al.  Microfluidic multipoles theory and applications , 2018, Nature Communications.

[125]  Douglas A. Lauffenburger,et al.  Polyfunctional responses by human T cells result from sequential release of cytokines , 2011, Proceedings of the National Academy of Sciences.

[126]  Dong Sun,et al.  A fluorescent microbead-based microfluidic immunoassay chip for immune cell cytokine secretion quantification. , 2018, Lab on a chip.

[127]  Valentin Romanov,et al.  A critical comparison of protein microarray fabrication technologies. , 2014, The Analyst.

[128]  Daniel Bratton,et al.  Development of quantitative cell-based enzyme assays in microdroplets. , 2008, Analytical chemistry.

[129]  David R Walt,et al.  Protein Counting in Single Cancer Cells. , 2016, Analytical chemistry.

[130]  Bifeng Liu,et al.  Agarose-based microwell array chip for high-throughput screening of functional microorganisms. , 2019, Talanta.

[131]  J. C. Love,et al.  A microengraving method for rapid selection of single cells producing antigen-specific antibodies , 2006, Nature Biotechnology.

[132]  Xiangmin Zhang,et al.  Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling. , 2018, Analytical chemistry.

[133]  Shih-Chung Wei,et al.  Smart Hydrogel Microfluidics for Single-Cell Multiplexed Secretomic Analysis with High Sensitivity. , 2018, Small.

[134]  James R Heath,et al.  Quantitating cell-cell interaction functions with applications to glioblastoma multiforme cancer cells. , 2012, Nano letters.

[135]  Kermit K. Murray,et al.  Microfluidic chips for mass spectrometry-based proteomics. , 2009, Journal of mass spectrometry : JMS.

[136]  Marissa Fessenden,et al.  Technologies to watch in 2019 , 2019, Nature.

[137]  Stavros Stavrakis,et al.  High-throughput microfluidic imaging flow cytometry. , 2019, Current opinion in biotechnology.

[138]  Haifang Li,et al.  Cell signaling analysis by mass spectrometry under coculture conditions on an integrated microfluidic device. , 2011, Analytical chemistry.

[139]  J. Heath,et al.  Chemical methods for the simultaneous quantitation of metabolites and proteins from single cells. , 2015, Journal of the American Chemical Society.

[140]  Bifeng Liu,et al.  Dynamic Microfluidic Cytometry for Single-Cell Cellomics: High-Throughput Probing Single-Cell-Resolution Signaling. , 2018, Analytical chemistry.

[141]  Wu Liu,et al.  Online monodisperse droplets based liquid–liquid extraction on a continuously flowing system by using microfluidic devices , 2014 .

[142]  Jin‐Ming Lin,et al.  Measurement of Cell-Matrix Adhesion at Single-Cell Resolution for Revealing the Functions of Biomaterials for Adherent Cell Culture. , 2018, Analytical chemistry.

[143]  Haifang Li,et al.  Strategy for signaling molecule detection by using an integrated microfluidic device coupled with mass spectrometry to study cell-to-cell communication. , 2013, Analytical chemistry.