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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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Xie Y, Chen Z, Cai D, Huang D, Huang E, Yang X, Zhang T, Wen H, Wang Y, Zhao M, Liu D, Xu B. Rapid Detection of Uropathogens Using an Integrated Multiplex Digital Nucleic Acid Detection Assay Powered by a Digital-to-Droplet Microfluidic Device. Anal Chem 2024. [PMID: 39018349 DOI: 10.1021/acs.analchem.4c02578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
The digital nucleic acid detection assay features the capability of absolute quantitation without the need for calibration, thereby facilitating the rapid identification of pathogens. Although several integrated digital nucleic acid detection techniques have been developed, there are still constraints in terms of automation and analysis throughput. To tackle these challenges, this study presents a digital-to-droplet microfluidic device comprising a digital microfluidics (DMF) module at the bottom and a droplet microfluidics module at the top. Following sample introduction, the extraction of nucleic acid and the dispensation of nucleic acid elution for mixing with the multiple amplification reagents are carried out in the DMF module. Subsequently, the reaction droplets are transported to the sample inlet of the droplet microfluidic module via a liquid outlet, and then droplet generation in four parallel units within the droplet microfluidics module is actuated by negative pressure generated by a syringe vacuum. The digital-to-droplet microfluidic device was employed to execute an integrated multiplex digital droplet nucleic acid detection assay (imDDNA) incorporating loop-mediated isothermal amplification (LAMP). This assay was specifically designed to enable simultaneous detection of four uropathogens, namely, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecalis. The entire process of the imDDNA is completed within 75 min, with a detection range spanning 5 orders of magnitude (9.43 × 10-2.86 × 104 copies μL-1). The imDDNA was employed for the detection of batched clinical specimens, showing a consistency of 91.1% when compared with that of the conventional method. The imDDNA exhibits simplicity in operation and accuracy in quantification, thus offering potential advantages in achieving rapid pathogen detection.
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Affiliation(s)
- Yang Xie
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Zhenhua Chen
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
| | - Dongyang Cai
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
| | - Dezhi Huang
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Enqi Huang
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Xiao Yang
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
| | - Ting Zhang
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
| | - Hongting Wen
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
| | - Yu Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Meng Zhao
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Dayu Liu
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
| | - Banglao Xu
- Department of Laboratory Medicine, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510180, China
- Guangdong Engineering Technology Research Center of Microfluidic Chip Medical Diagnosis, Guangzhou 510180, China
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3
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Gebreyesus ST, Muneer G, Huang CC, Siyal AA, Anand M, Chen YJ, Tu HL. Recent advances in microfluidics for single-cell functional proteomics. LAB ON A CHIP 2023; 23:1726-1751. [PMID: 36811978 DOI: 10.1039/d2lc01096h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Single-cell proteomics (SCP) reveals phenotypic heterogeneity by profiling individual cells, their biological states and functional outcomes upon signaling activation that can hardly be probed via other omics characterizations. This has become appealing to researchers as it enables an overall more holistic view of biological details underlying cellular processes, disease onset and progression, as well as facilitates unique biomarker identification from individual cells. Microfluidic-based strategies have become methods of choice for single-cell analysis because they allow facile assay integrations, such as cell sorting, manipulation, and content analysis. Notably, they have been serving as an enabling technology to improve the sensitivity, robustness, and reproducibility of recently developed SCP methods. Critical roles of microfluidics technologies are expected to further expand rapidly in advancing the next phase of SCP analysis to reveal more biological and clinical insights. In this review, we will capture the excitement of the recent achievements of microfluidics methods for both targeted and global SCP, including efforts to enhance the proteomic coverage, minimize sample loss, and increase multiplexity and throughput. Furthermore, we will discuss the advantages, challenges, applications, and future prospects of SCP.
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Affiliation(s)
- Sofani Tafesse Gebreyesus
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | | | - Asad Ali Siyal
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
| | - Mihir Anand
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan.
- Nano Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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4
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Abstract
This paper reviews methods for detecting proteins based on molecular digitization, i.e., the isolation and detection of single protein molecules or singulated ensembles of protein molecules. The single molecule resolution of these methods has resulted in significant improvements in the sensitivity of immunoassays beyond what was possible using traditional "analog" methods: the sensitivity of some digital immunoassays approach those of methods for measuring nucleic acids, such as the polymerase chain reaction (PCR). The greater sensitivity of digital protein detection has resulted in immuno-diagnostics with high potential societal impact, e.g., the early diagnosis and therapeutic intervention of Alzheimer's Disease. In this review, we will first provide the motivation for developing digital protein detection methods given the limitations in the sensitivity of analog methods. We will describe the paradigm shift catalyzed by single molecule detection, and will describe in detail one digital approach - which we call digital bead assays (DBA) - based on the capture and labeling of proteins on beads, identifying "on" and "off" beads, and quantification using Poisson statistics. DBA based on the single molecule array (Simoa) technology have sensitivities down to attomolar concentrations, equating to ∼10 proteins in a 200 μL sample. We will describe the concept behind DBA, the different single molecule labels used, the ways of analyzing beads (imaging of arrays and flow), the binding reagents and substrates used, and integration of these technologies into fully automated and miniaturized systems. We provide an overview of emerging approaches to digital protein detection, including those based on digital detection of nucleic acids labels, single nanoparticle detection, measurements using nanopores, and methods that exploit the kinetics of single molecule binding. We outline the initial impact of digital protein detection on clinical measurements, highlighting the importance of customized assay development and translational clinical research. We highlight the use of DBA in the measurement of neurological protein biomarkers in blood, and how these higher sensitivity methods are changing the diagnosis and treatment of neurological diseases. We conclude by summarizing the status of digital protein detection and suggest how the lab-on-a-chip community might drive future innovations in this field.
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Affiliation(s)
- David C Duffy
- Quanterix Corporation, 900 Middlesex Turnpike, Billerica, MA 01821, USA.
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5
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Chowdhury T, Cressiot B, Parisi C, Smolyakov G, Thiébot B, Trichet L, Fernandes FM, Pelta J, Manivet P. Circulating Tumor Cells in Cancer Diagnostics and Prognostics by Single-Molecule and Single-Cell Characterization. ACS Sens 2023; 8:406-426. [PMID: 36696289 DOI: 10.1021/acssensors.2c02308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Circulating tumor cells (CTCs) represent an interesting source of biomarkers for diagnosis, prognosis, and the prediction of cancer recurrence, yet while they are extensively studied in oncobiology research, their diagnostic utility has not yet been demonstrated and validated. Their scarcity in human biological fluids impedes the identification of dangerous CTC subpopulations that may promote metastatic dissemination. In this Perspective, we discuss promising techniques that could be used for the identification of these metastatic cells. We first describe methods for isolating patient-derived CTCs and then the use of 3D biomimetic matrixes in their amplification and analysis, followed by methods for further CTC analyses at the single-cell and single-molecule levels. Finally, we discuss how the elucidation of mechanical and morphological properties using techniques such as atomic force microscopy and molecular biomarker identification using nanopore-based detection could be combined in the future to provide patients and their healthcare providers with a more accurate diagnosis.
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Affiliation(s)
- Tafsir Chowdhury
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Cleo Parisi
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Georges Smolyakov
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France
| | | | - Léa Trichet
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Francisco M Fernandes
- Sorbonne Université, UMR 7574, Laboratoire de Chimie de la Matière Condensée de Paris, 75005 Paris, France
| | - Juan Pelta
- CY Cergy Paris Université, CNRS, LAMBE, 95000 Cergy, France.,Université Paris-Saclay, Université d'Evry, CNRS, LAMBE, 91190 Evry, France
| | - Philippe Manivet
- Centre de Ressources Biologiques Biobank Lariboisière (BB-0033-00064), DMU BioGem, AP-HP, 75010 Paris, France.,Université Paris Cité, Inserm, NeuroDiderot, F-75019 Paris, France
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6
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Liu W, Zhang R, Huang S, Li X, Liu W, Zhou J, Zhu L, Song Y, Yang C. Quantification of Intracellular Proteins in Single Cells Based on Engineered Picoliter Droplets. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7929-7937. [PMID: 35748862 DOI: 10.1021/acs.langmuir.2c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Unlike conventional bulk measurements, single-cell protein analysis permits quantification of protein expression in individual cells. This has shed light on the cell-to-cell variation in heterogeneous biological systems, such as solid tumors, brain tissues, and developing embryos. Herein, a microfluidic method is developed to profile protein expression in individual cells by performing single-cell intracellular protein immunoassay in picoliter paired droplets. The high sensitivity of single-cell protein analysis on a chip is achieved by the confined reaction volume of picoliter droplets, efficient kinetic characteristics of the immunoassay through active mixing, and minimum single-cell protein loss by integrated operations. The abundance of an intracellular prostate specific antigen at the single-cell level is measured, and then the platform is applied to identify cell types and investigate heterogeneity within cell populations. Overall, a paired chip for single-cell immunoassay establishes a foundation for parallel, sensitive, and integrated protein quantification at the single-cell level and will find wide applications in the field of single-cell proteomics.
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Affiliation(s)
- Weizhi Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ruihua Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shanqing Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xingrui Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wanling Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jianhui Zhou
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lin Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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7
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Cruz Villarreal J, Kruithoff R, Egatz-Gomez A, Coleman PD, Ros R, Sandrin TR, Ros A. MIMAS: microfluidic platform in tandem with MALDI mass spectrometry for protein quantification from small cell ensembles. Anal Bioanal Chem 2022; 414:3945-3958. [PMID: 35385983 PMCID: PMC9188328 DOI: 10.1007/s00216-022-04038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/26/2022]
Abstract
Understanding cell-to-cell variation at the molecular level provides relevant information about biological phenomena and is critical for clinical and biological research. Proteins carry important information not available from single-cell genomics and transcriptomics studies; however, due to the minute amount of proteins in single cells and the complexity of the proteome, quantitative protein analysis at the single-cell level remains challenging. Here, we report an integrated microfluidic platform in tandem with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) for the detection and quantification of targeted proteins from small cell ensembles (> 10 cells). All necessary steps for the assay are integrated on-chip including cell lysis, protein immunocapture, tryptic digestion, and co-crystallization with the matrix solution for MALDI-MS analysis. We demonstrate that our approach is suitable for protein quantification by assessing the apoptotic protein Bcl-2 released from MCF-7 breast cancer cells, ranging from 26 to 223 cells lysed on-chip (8.75 nL wells). A limit of detection (LOD) of 11.22 nM was determined, equivalent to 5.91 × 107 protein molecules per well. Additionally, the microfluidic platform design was further improved, establishing the successful quantification of Bcl-2 protein from MCF-7 cell ensembles ranging from 8 to 19 cells in 4 nL wells. The LOD in the smaller well designs for Bcl-2 resulted in 14.85 nM, equivalent to 3.57 × 107 protein molecules per well. This work shows the capability of our approach to quantitatively assess proteins from cell lysate on the MIMAS platform for the first time. These results demonstrate our approach constitutes a promising tool for quantitative targeted protein analysis from small cell ensembles down to single cells, with the capability for multiplexing through parallelization and automation.
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Affiliation(s)
- Jorvani Cruz Villarreal
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Rory Kruithoff
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
| | - Ana Egatz-Gomez
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paul D Coleman
- School of Life Sciences, Arizona State University, Temple, AZ, USA
- ASU-Banner Neurodegenerative Research Center, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Robert Ros
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, AZ, USA
- Center for Single Molecule Biophysics, The Biodesign Institute, Arizona State University, Temple, AZ, USA
| | - Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ, USA
- Julie Ann Wrigley Global Futures Laboratory, Arizona State University, Tempe, AZ, USA
| | - Alexandra Ros
- School of Molecular Sciences, Arizona State University, Temple, AZ, USA.
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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8
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Wang C, Wang C, Wu Y, Gao J, Han Y, Chu Y, Qiang L, Qiu J, Gao Y, Wang Y, Song F, Wang Y, Shao X, Zhang Y, Han L. High-Throughput, Living Single-Cell, Multiple Secreted Biomarker Profiling Using Microfluidic Chip and Machine Learning for Tumor Cell Classification. Adv Healthc Mater 2022; 11:e2102800. [PMID: 35368151 DOI: 10.1002/adhm.202102800] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/02/2022] [Indexed: 11/09/2022]
Abstract
Secreted proteins provide abundant functional information on living cells and can be used as important tumor diagnostic markers, of which profiling at the single-cell level is helpful for accurate tumor cell classification. Currently, achieving living single-cell multi-index, high-sensitivity, and quantitative secretion biomarker profiling remains a great challenge. Here, a high-throughput living single-cell multi-index secreted biomarker profiling platform is proposed, combined with machine learning, to achieve accurate tumor cell classification. A single-cell culture microfluidic chip with self-assembled graphene oxide quantum dots (GOQDs) enables high-activity single-cell culture, ensuring normal secretion of biomarkers and high-throughput single-cell separation, providing sufficient statistical data for machine learning. At the same time, the antibody barcode chip with self-assembled GOQDs performs multi-index, highly sensitive, and quantitative detection of secreted biomarkers, in which each cell culture chamber covers a whole barcode array. Importantly, by combining the K-means strategy with machine learning, thousands of single tumor cell secretion data are analyzed, enabling tumor cell classification with a recognition accuracy of 95.0%. In addition, further profiling of the grouping results reveals the unique secretion characteristics of subgroups. This work provides an intelligent platform for high-throughput living single-cell multiple secretion biomarker profiling, which has broad implications for cancer investigation and biomedical research.
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Affiliation(s)
- Chao Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Chunhua Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yu Wu
- Obstetrics and Gynecology Department Peking University Third Hospital Beijing 100191 China
| | - Jianwei Gao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yingkuan Han
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yujin Chu
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Le Qiang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Jiaoyan Qiu
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yakun Gao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yanhao Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Fangteng Song
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yihe Wang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Xiaowei Shao
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Yu Zhang
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
| | - Lin Han
- Institute of Marine Science and Technology Shandong University Tsingdao 266237 China
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9
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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10
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Prostate Cancer Biomarkers: From diagnosis to prognosis and precision-guided therapeutics. Pharmacol Ther 2021; 228:107932. [PMID: 34174272 DOI: 10.1016/j.pharmthera.2021.107932] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022]
Abstract
Prostate cancer (PCa) is one of the most commonly diagnosed malignancies and among the leading causes of cancer-related death worldwide. It is a highly heterogeneous disease, ranging from remarkably slow progression or inertia to highly aggressive and fatal disease. As therapeutic decision-making, clinical trial design and outcome highly depend on the appropriate stratification of patients to risk groups, it is imperative to differentiate between benign versus more aggressive states. The incorporation of clinically valuable prognostic and predictive biomarkers is also potentially amenable in this process, in the timely prevention of metastatic disease and in the decision for therapy selection. This review summarizes the progress that has so far been made in the identification of the genomic events that can be used for the classification, prediction and prognostication of PCa, and as major targets for clinical intervention. We include an extensive list of emerging biomarkers for which there is enough preclinical evidence to suggest that they may constitute crucial targets for achieving significant advances in the management of the disease. Finally, we highlight the main challenges that are associated with the identification of clinically significant PCa biomarkers and recommend possible ways to overcome such limitations.
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11
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Huang Q, Li N, Zhang H, Che C, Sun F, Xiong Y, Canady TD, Cunningham BT. Critical Review: digital resolution biomolecular sensing for diagnostics and life science research. LAB ON A CHIP 2020; 20:2816-2840. [PMID: 32700698 PMCID: PMC7485136 DOI: 10.1039/d0lc00506a] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the frontiers in the field of biosensors is the ability to quantify specific target molecules with enough precision to count individual units in a test sample, and to observe the characteristics of individual biomolecular interactions. Technologies that enable observation of molecules with "digital precision" have applications for in vitro diagnostics with ultra-sensitive limits of detection, characterization of biomolecular binding kinetics with a greater degree of precision, and gaining deeper insights into biological processes through quantification of molecules in complex specimens that would otherwise be unobservable. In this review, we seek to capture the current state-of-the-art in the field of digital resolution biosensing. We describe the capabilities of commercially available technology platforms, as well as capabilities that have been described in published literature. We highlight approaches that utilize enzymatic amplification, nanoparticle tags, chemical tags, as well as label-free biosensing methods.
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Affiliation(s)
- Qinglan Huang
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Nantao Li
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Hanyuan Zhang
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Congnyu Che
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Fu Sun
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Taylor D. Canady
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Brian T. Cunningham
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, 208 North Wright Street, Urbana, IL 61801
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Department of Bioengineering, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- Illinois Cancer Center, University of Illinois at Urbana-Champaign Urbana, IL 61801
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12
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Labib M, Philpott DN, Wang Z, Nemr C, Chen JB, Sargent EH, Kelley SO. Magnetic Ranking Cytometry: Profiling Rare Cells at the Single-Cell Level. Acc Chem Res 2020; 53:1445-1457. [PMID: 32662263 DOI: 10.1021/acs.accounts.0c00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cellular heterogeneity in biological systems presents major challenges in the diagnosis and treatment of disease and also complicates the deconvolution of complex cellular phenomena. Single-cell analysis methods provide information that is not masked by the intrinsic heterogeneity of the bulk population and can therefore be applied to gain insights into heterogeneity among different cell subpopulations with fine resolution. Over the last 5 years, an explosion in the number of single-cell measurement methods has occurred. However, most of these methods are applicable to pure populations of cultured cells and are not able to handle high levels of phenotypic heterogeneity or a large background of nontarget cells. Microfluidics is an attractive tool for single cell manipulation as it enables individual encasing of single cells, allowing for high-throughput analysis with precise control of the local environment. Our laboratory has developed a new microfluidics-based analytical strategy to meet this unmet need referred to as magnetic ranking cytometry (MagRC). Cells expressing a biomarker of interest are labeled with receptor-coated magnetic nanoparticles and isolated from nontarget cells using a microfluidic device. The device ranks the cells according to the level of bound magnetic nanoparticles, which corresponds to the expression level of a target biomarker. Over the last several years, two generations of MagRC devices have been developed for different applications. The first-generation MagRC devices are powerful tools for the quantitation and analysis of rare cells present in heterogeneous samples, such as circulating tumor cells, stem cells, and pathogenic bacteria. The second-generation MagRC devices are compatible with the efficient recovery of cells sorted on the basis of protein expression and can be used to analyze large populations of cells and perform phenotypic CRISPR screens. To improve analytical precision, newer iterations of the first-generation and second-generation MagRC devices have been integrated with electrochemical sensors and Hall effect sensors, respectively. Both generations of MagRC devices permit the isolation of viable cells, which sets the stage for a wide range of applications, such as generating cell lines from rare cells and in vitro screening for effective therapeutic interventions in cancer patients to realize the promise of personalized medicine. This Account summarizes the development and application of the MagRC and describes a suite of advances that have enabled single-cell tumor cell analysis and monitoring tumor response to therapy, stem cell analysis, and detection of pathogens.
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Affiliation(s)
- Mahmoud Labib
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - David N. Philpott
- Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Zongjie Wang
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Carine Nemr
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Jenise B. Chen
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Edward H. Sargent
- Department of Electrical & Computer Engineering, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Shana O. Kelley
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Institute for Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G4, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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13
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Liu L, Chen D, Wang J, Chen J. Advances of Single-Cell Protein Analysis. Cells 2020; 9:E1271. [PMID: 32443882 PMCID: PMC7290353 DOI: 10.3390/cells9051271] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 02/07/2023] Open
Abstract
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.
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Affiliation(s)
- Lixing Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deyong Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junbo Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China; (L.L.); (D.C.)
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- School of Future Technologies, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Ho D, Quake SR, McCabe ERB, Chng WJ, Chow EK, Ding X, Gelb BD, Ginsburg GS, Hassenstab J, Ho CM, Mobley WC, Nolan GP, Rosen ST, Tan P, Yen Y, Zarrinpar A. Enabling Technologies for Personalized and Precision Medicine. Trends Biotechnol 2020; 38:497-518. [PMID: 31980301 PMCID: PMC7924935 DOI: 10.1016/j.tibtech.2019.12.021] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023]
Abstract
Individualizing patient treatment is a core objective of the medical field. Reaching this objective has been elusive owing to the complex set of factors contributing to both disease and health; many factors, from genes to proteins, remain unknown in their role in human physiology. Accurately diagnosing, monitoring, and treating disorders requires advances in biomarker discovery, the subsequent development of accurate signatures that correspond with dynamic disease states, as well as therapeutic interventions that can be continuously optimized and modulated for dose and drug selection. This work highlights key breakthroughs in the development of enabling technologies that further the goal of personalized and precision medicine, and remaining challenges that, when addressed, may forge unprecedented capabilities in realizing truly individualized patient care.
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Affiliation(s)
- Dean Ho
- The N.1 Institute for Health (N.1), National University of Singapore, Singapore; The Institute for Digital Medicine (WisDM), National University of Singapore, Singapore; Department of Biomedical Engineering, NUS Engineering, National University of Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, CA, USA; Department of Applied Physics, Stanford University, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Wee Joo Chng
- Department of Haematology and Oncology, National University Cancer Institute, National University Health System, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Edward K Chow
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Xianting Ding
- Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Geoffrey S Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, NC, USA
| | - Jason Hassenstab
- Department of Neurology, Washington University in St. Louis, MO, USA; Psychological & Brain Sciences, Washington University in St. Louis, MO, USA
| | - Chih-Ming Ho
- Department of Mechanical Engineering, University of California, Los Angeles, CA, USA
| | - William C Mobley
- Department of Neurosciences, University of California, San Diego, CA, USA
| | - Garry P Nolan
- Department of Microbiology & Immunology, Stanford University, CA, USA
| | - Steven T Rosen
- Comprehensive Cancer Center and Beckman Research Institute, City of Hope, CA, USA
| | - Patrick Tan
- Duke-NUS Medical School, National University of Singapore, Singapore
| | - Yun Yen
- College of Medical Technology, Center of Cancer Translational Research, Taipei Cancer Center of Taipei Medical University, Taipei, Taiwan
| | - Ali Zarrinpar
- Department of Surgery, Division of Transplantation & Hepatobiliary Surgery, University of Florida, FL, USA
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15
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Mejía-Salazar JR, Rodrigues Cruz K, Materón Vásques EM, Novais de Oliveira Jr. O. Microfluidic Point-of-Care Devices: New Trends and Future Prospects for eHealth Diagnostics. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1951. [PMID: 32244343 PMCID: PMC7180826 DOI: 10.3390/s20071951] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/09/2020] [Accepted: 03/20/2020] [Indexed: 12/15/2022]
Abstract
Point-of-care (PoC) diagnostics is promising for early detection of a number of diseases, including cancer, diabetes, and cardiovascular diseases, in addition to serving for monitoring health conditions. To be efficient and cost-effective, portable PoC devices are made with microfluidic technologies, with which laboratory analysis can be made with small-volume samples. Recent years have witnessed considerable progress in this area with "epidermal electronics", including miniaturized wearable diagnosis devices. These wearable devices allow for continuous real-time transmission of biological data to the Internet for further processing and transformation into clinical knowledge. Other approaches include bluetooth and WiFi technology for data transmission from portable (non-wearable) diagnosis devices to cellphones or computers, and then to the Internet for communication with centralized healthcare structures. There are, however, considerable challenges to be faced before PoC devices become routine in the clinical practice. For instance, the implementation of this technology requires integration of detection components with other fluid regulatory elements at the microscale, where fluid-flow properties become increasingly controlled by viscous forces rather than inertial forces. Another challenge is to develop new materials for environmentally friendly, cheap, and portable microfluidic devices. In this review paper, we first revisit the progress made in the last few years and discuss trends and strategies for the fabrication of microfluidic devices. Then, we discuss the challenges in lab-on-a-chip biosensing devices, including colorimetric sensors coupled to smartphones, plasmonic sensors, and electronic tongues. The latter ones use statistical and big data analysis for proper classification. The increasing use of big data and artificial intelligence methods is then commented upon in the context of wearable and handled biosensing platforms for the Internet of things and futuristic healthcare systems.
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Affiliation(s)
| | - Kamilla Rodrigues Cruz
- National Institute of Telecommunications (Inatel), 37540-000 Santa Rita do Sapucaí, MG, Brazil;
| | - Elsa María Materón Vásques
- Sao Carlos Institute of Physics, University of Sao Paulo, P.O. Box 369, 13560-970 Sao Carlos, SP, Brazil; (E.M.M.V.); (O.N.d.O.J.)
- Chemistry Department, Federal University of São Carlos, CP 676, São Carlos 13565-905, São Paulo, Brazil
| | - Osvaldo Novais de Oliveira Jr.
- Sao Carlos Institute of Physics, University of Sao Paulo, P.O. Box 369, 13560-970 Sao Carlos, SP, Brazil; (E.M.M.V.); (O.N.d.O.J.)
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16
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Wu C, Maley AM, Walt DR. Single-molecule measurements in microwells for clinical applications. Crit Rev Clin Lab Sci 2019:1-21. [PMID: 31865834 DOI: 10.1080/10408363.2019.1700903] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to detect and analyze proteins, nucleic acids, and other biomolecules is critical for clinical diagnostics and for understanding the underlying mechanisms of disease. Current detection methods in clinical and research laboratories rely upon bulk measurement techniques such as immunoassays, polymerase chain reaction, and mass spectrometry to detect these biomarkers. However, many potentially useful protein or nucleic acid biomarkers in blood, saliva, or other biofluids exist at concentrations well below the detection limits of current methods, necessitating the development of more sensitive technologies. Single-molecule measurements are poised to address this challenge, vastly improving sensitivity for detecting low abundance biomarkers and rare events within a population. Microwell arrays have emerged as a powerful tool for single-molecule measurements, enabling ultrasensitive detection of disease-relevant biomolecules in easily accessible biofluids. This review discusses the development, fundamentals, and clinical applications of microwell-based single-molecule methods, as well as challenges and future directions for translating these methods to the clinic.
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Affiliation(s)
- Connie Wu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Adam M Maley
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - David R Walt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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17
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Shi M, Geng X, Wang C, Guan Y. Quantification of Low Copy Number Proteins in Single Cells. Anal Chem 2019; 91:11493-11496. [PMID: 31476854 DOI: 10.1021/acs.analchem.9b02989] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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.
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Affiliation(s)
- Meng Shi
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China.,University of Chinese Academy of Sciences , Beijing 100049 , P.R. China
| | - Xuhui Geng
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
| | - Chengye Wang
- Department of Thoracic Surgery , The Second Hospital of Dalian Medical University , No. 467, Zhongshan Road , Dalian , Liaoning 116023 , China
| | - Yafeng Guan
- Department of Instrumentation & Analytical Chemistry, CAS Key Laboratory of Separation Sciences for Analytical Chemistry , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
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18
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Chen P, Chen D, Li S, Ou X, Liu BF. Microfluidics towards single cell resolution protein analysis. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.06.022] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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19
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Liu Y, Chen X, Zhang Y, Liu J. Advancing single-cell proteomics and metabolomics with microfluidic technologies. Analyst 2019; 144:846-858. [PMID: 30351310 DOI: 10.1039/c8an01503a] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Recent advances in single-cell analysis have unraveled substantial heterogeneity among seemingly identical cells at genomic and transcriptomic levels. These discoveries have urged scientists to develop new tools that are capable of investigating single cells from a broader set of "omics". Proteomics and metabolomics, for instance, are of particular interest as they are closely correlated with a dynamic picture of cellular behaviors and phenotypic identities. The development of such tools requires highly efficient isolation and processing of a large number of individual cells, where techniques such as microfluidics are extremely useful. Here, we review the recent advances in single-cell proteomics and metabolomics, with a focus on microfluidics-based platforms. We highlight a vast array of emerging microfluidic formats for single-cell isolation and manipulation, and how the state-of-the-art analytical tools are coupled with such platforms for proteomic and metabolomic profiling.
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Affiliation(s)
- Yifan Liu
- Jiangsu Key Laboratory for Carbon-based Functional Materials and Devices, Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu Province 215123, China.
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20
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Power-free polydimethylsiloxane femtoliter-sized arrays for bead-based digital immunoassays. Biosens Bioelectron 2019; 139:111339. [PMID: 31132722 DOI: 10.1016/j.bios.2019.111339] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 01/01/2023]
Abstract
A novel microfluidic chip employing power-free polydimethylsiloxane (PDMS) femtoliter-sized arrays was developed for the detection of low concentrations of protein biomakers by isolating individual paramagnetic beads in single wells. Arrays of femtoliter-sized wells were fabricated with PDMS using well-developed molding techniques. Paramagnetic beads were functionalized with specific antibodies to capture the antigens. These antigens were labeled with enzymes via conventional multistep immunosandwich approach. After suspending in aqueous solutions of enzyme substrate, the solutions were delivered to the arrays using a conventional micropipette. The aqueous solutions were introduced into the microwells by capillarity and the beads were loaded into microwells by gravity. A fluorocarbon oil was then flowed into the chip to remove excess beads from the surface of the array and meanwhile isolated the femtoliter-sized wells. All processes were achieved by conventional micropipette, without external pumping systems and valves. Finally, the arrays were imaged using standard fluorescence imaging after incubation 30 min for digital counting enzyme molecules. It was demonstrated that the chip platform possessed the performance of digital counting with a linear dynamic range from 1 aM to 1 fM for the detection of biotinylated β-galactosidase (BβG), achieving a limit of detection (LOD) of 930 zM. Using this chip, a digital immunoassay to detect Tumor Necrosis Factor α (TNF- α) was developed. Since the chip fabrication is low-cost and circumvents the surface modification, we expect it can become a new chip-based digital immunoassay platform for ultrasensitive diagnostic of biomarkers.
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21
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Tabata KV, Minagawa Y, Kawaguchi Y, Ono M, Moriizumi Y, Yamayoshi S, Fujioka Y, Ohba Y, Kawaoka Y, Noji H. Antibody-free digital influenza virus counting based on neuraminidase activity. Sci Rep 2019; 9:1067. [PMID: 30705374 PMCID: PMC6355933 DOI: 10.1038/s41598-018-37994-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/17/2018] [Indexed: 12/14/2022] Open
Abstract
There is large demand for a quantitative method for rapid and ultra-sensitive detection of the influenza virus. Here, we established a digital influenza virus counting (DIViC) method that can detect a single virion without antibody. In the assay, a virion is stochastically entrapped inside a femtoliter reactor array device for the fluorogenic assay of neuraminidase, and incubated for minutes. By analyzing 600,000 reactors, the practical limit of detection reached the order of 103 (PFU)/mL, only 10-times less sensitive than RT-PCR and more than 1000-times sensitive than commercial rapid test kits (RIDTs). Interestingly, neuraminidase activity differed among virions. The coefficient of variance was 30-40%, evidently broader than that of alkaline phosphatase measured as a model enzyme for comparison, suggesting the heterogeneity in size and integrity among influenza virus particles. Sensitivity to oseltamivir also differed between virions. We also tested DIViC using clinical gargle samples that imposes less burden for sampling while with less virus titre. The comparison with RIDTs showed that DIViC was largely superior to RIDTs in the sensitivity with the clinical samples although a few false-positive signals were observed in some clinical samples that remains as a technical challenge.
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Affiliation(s)
- Kazuhito V Tabata
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
- ImPACT Program, Cabinet Office, Government of Japan, Chiyoda-ku, Tokyo, 100-8914, Japan.
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan
| | - Yuko Kawaguchi
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan
| | - Mana Ono
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan
| | - Yoshiki Moriizumi
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan
| | - Seiya Yamayoshi
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
| | - Yoichiro Fujioka
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-ku, Sapporo, Japan
| | - Yusuke Ohba
- Department of Cell Physiology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, N15 W7, Kita-ku, Sapporo, Japan
| | - Yoshihiro Kawaoka
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639, Japan
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, 53711, USA
| | - Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Japan.
- ImPACT Program, Cabinet Office, Government of Japan, Chiyoda-ku, Tokyo, 100-8914, Japan.
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22
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Gou T, Hu J, Zhou S, Wu W, Fang W, Sun J, Hu Z, Shen H, Mu Y. A new method using machine learning for automated image analysis applied to chip-based digital assays. Analyst 2019; 144:3274-3281. [DOI: 10.1039/c9an00149b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
An automated machine learning based method for image processes applied to digital assays.
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Affiliation(s)
- Tong Gou
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Jiumei Hu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Shufang Zhou
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Wenshuai Wu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Weibo Fang
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Jingjing Sun
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Zhenming Hu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Haotian Shen
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
| | - Ying Mu
- Research Center for Analytical Instrumentation
- Institute of Cyber-Systems and Control
- State Key Laboratory of Industrial Control Technology
- College of Control Science and Engineering
- Zhejiang University
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23
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Shao X, Wang X, Guan S, Lin H, Yan G, Gao M, Deng C, Zhang X. Integrated Proteome Analysis Device for Fast Single-Cell Protein Profiling. Anal Chem 2018; 90:14003-14010. [PMID: 30375851 DOI: 10.1021/acs.analchem.8b03692] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In our previous work, we have demonstrated an integrated proteome analysis device (iPAD-100) to analyze proteomes from 100 cells. (1) In this work, for the first time, a novel integrated device for single-cell analysis (iPAD-1) was developed to profile proteins in a single cell within 1 h. In the iPAD-1, a selected single cell was directly sucked into a 22 μm i.d. capillary. Then the cell lysis and protein digestion were simultaneously accomplished in the capillary in a 2 nL volume, which could prevent protein loss and excessive dilution. Digestion was accelerated by using elevated temperature with ultrasonication. The whole time of cell treatment was 30 min. After that, single-cell digest peptides were transferred into an LC column directly through a true zero dead volume union, to minimize protein transfer loss. A homemade 22 μm i.d. nano-LC packing column with 3 μm i.d. ESI tip was used in the device to achieve ultrasensitive detection. A 30 min elution program was applied to analysis of the single-cell proteome. Therefore, the total time needed for a single-cell analysis was only 1 h. In an analysis of 10 single HeLa cells, a maximum of 328 proteins were identified in one cell by using an Orbitrap Fusion Tribrid MS instrument, and the detection limit was estimated at around 1.7-170 zmol. Such a sensitivity of the iPAD-1 was ∼120-fold higher than that of our previously developed iPAD-100 system. (1) Prominent cellular heterogeneity in protein expressive profiling was observed. Furthermore, we roughly estimated the phases of the cell cycle of tested HeLa cells by the amount of core histone proteins.
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Affiliation(s)
- Xi Shao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xuantang Wang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Sheng Guan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Haizhu Lin
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Guoquan Yan
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences , Fudan University , Shanghai 200433 , People's Republic of China
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24
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Saxena A, Dagur PK, Desai A, McCoy JP. Ultrasensitive Quantification of Cytokine Proteins in Single Lymphocytes From Human Blood Following ex-vivo Stimulation. Front Immunol 2018; 9:2462. [PMID: 30405640 PMCID: PMC6206239 DOI: 10.3389/fimmu.2018.02462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022] Open
Abstract
In this study we demonstrate the feasibility of direct, quantitative measurement of cytokine proteins in single human CD8 lymphocytes from fresh peripheral blood of healthy donors following a brief ex vivo stimulation. Cytokine-secreting cells were identified using cell surface “catch” reagents and single cell data were obtained by sorting of individual cytokine-secreting cells into 96 well plates containing lysis buffer followed by analysis using ultrasensitive immunoassays for interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). CD8 cells negative for cytokine production, as determined by the cell surface catch reagents were used as negative controls. Furthermore, studies were undertaken to compare the mean fluorescence intensity (MFI) values of cytokine staining by flow cytometry with the quantification of cytokines using the current method. This study demonstrates that it is feasible to quantify cytokines from individual primary cells. A shift from qualitative to quantitative determinations of cytokine protein levels in single cells will permit more precise and reproducible studies of heterogeneity in the immune system and can be accomplished with readily available instrumentation.
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Affiliation(s)
- Ankit Saxena
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Pradeep K Dagur
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - Alisha Desai
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
| | - John Philip McCoy
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, United States
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25
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Li Z, Askim JR, Suslick KS. The Optoelectronic Nose: Colorimetric and Fluorometric Sensor Arrays. Chem Rev 2018; 119:231-292. [DOI: 10.1021/acs.chemrev.8b00226] [Citation(s) in RCA: 476] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zheng Li
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jon R. Askim
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Kenneth S. Suslick
- Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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26
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Affiliation(s)
- Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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27
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Kuo MS, Adam J, Dorvault N, Robin A, Friboulet L, Soria JC, Olaussen KA. A novel antibody-based approach to detect the functional ERCC1-202 isoform. DNA Repair (Amst) 2018; 64:34-44. [PMID: 29482102 DOI: 10.1016/j.dnarep.2018.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 10/26/2017] [Accepted: 02/06/2018] [Indexed: 12/16/2022]
Abstract
ERCC1/XPF endonuclease plays an important role in multiple DNA repair pathways and stands as a potential prognostic and predictive biomarker for cisplatin-based chemotherapy. Four distinct ERCC1 isoforms arising from alternative splicing have been described (201, 202, 203 and 204) but only the 202 isoform is functional in DNA excision repair, when interacting with its obligate partner XPF. Currently, there is no tool to assess specifically the expression of ERCC1-202 due to high sequence homology between the four isoforms. Here, we generated monoclonal antibodies directed against the heterodimer of ERCC1 and its obligate interacting partner XPF by genetic immunization. We obtained three monoclonal antibodies (2C11, 7C3 and 10D10) recognizing specifically the heterodimer ERCC1-202/XPF as well as the ERCC1-204/XPF with no affinity to ERCC1 or XPF monomers. By combining one of these three heterodimer-specific antibodies with a commercial anti-ERCC1 antibody (clone 4F9) unable to recognize the 204 isoform in a proximity ligation assay (PLA), we managed to specifically detect the functional ERCC1-202 isoform. This methodological breakthrough can constitute a basis for the development of clinical tests to evaluate ERCC1 functional proficiency.
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Affiliation(s)
- Mei-Shiue Kuo
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Julien Adam
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Nicolas Dorvault
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Angélique Robin
- UF de Pharmacologie Biologie, Saint Louis Hopital, Institut de Génétique Moléculaire, 75010, Paris, France
| | - Luc Friboulet
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Jean-Charles Soria
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France; Gustave Roussy, Université Paris-Saclay, Drug Development Department (DITEP), 94805, Villejuif, France
| | - Ken A Olaussen
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France.
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28
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Ashhurst TM, Smith AL, King NJC. High-Dimensional Fluorescence Cytometry. ACTA ACUST UNITED AC 2017; 119:5.8.1-5.8.38. [PMID: 29091263 DOI: 10.1002/cpim.37] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The immune system consists of a complex network of cells, all expressing a wide range of surface and/or intracellular proteins. Using flow cytometry, these cells can be analyzed by labeling with fluorophore-conjugated antibodies. The recent expansion of fluorescence flow cytometry technology, in conjunction with the ever-expanding understanding of the complexity of the immune system, has led to the generation of larger high-dimensional fluorescence flow cytometry panels. However, as panel size and complexity increases, so too does the difficulty involved in constructing high-quality panels, in addition to the challenges of analyzing such high-dimensional datasets. As such, this unit seeks to review the key principles involved in building high-dimensional panels, as well as to guide users through the process of building and analyzing quality panels. Here, cytometer configuration, fluorophore brightness, spreading error, antigen density, choosing the best conjugates, titration, optimization, and data analysis will all be addressed. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Thomas Myles Ashhurst
- Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia.,Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia.,Marie Bashir Institute for Emerging Infectious Disease (MBI), The University of Sydney, Sydney, Australia
| | - Adrian Lloyd Smith
- Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia
| | - Nicholas Jonathan Cole King
- Viral Immunopathology Laboratory, Discipline of Pathology, School of Medical Sciences, Sydney Medical School, The University of Sydney, Sydney, Australia.,Sydney Cytometry Facility, The University of Sydney and Centenary Institute, Sydney, Australia.,Ramaciotti Facility for Human Systems Biology (RFHSB), The University of Sydney and Centenary Institute, Sydney, Australia.,Marie Bashir Institute for Emerging Infectious Disease (MBI), The University of Sydney, Sydney, Australia.,Australian Institute for Nanoscale Science and Technology, The University of Sydney, Sydney, Australia
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29
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Su Y, Shi Q, Wei W. Single cell proteomics in biomedicine: High-dimensional data acquisition, visualization, and analysis. Proteomics 2017; 17. [PMID: 28128880 DOI: 10.1002/pmic.201600267] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 11/11/2022]
Abstract
New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data. The underlying assumptions, unique features, and limitations of the analytical methods with the designated biological questions they seek to answer will be discussed. Particular attention will be given to those information theoretical approaches that are anchored in a set of first principles of physics and can yield detailed (and often surprising) predictions.
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Affiliation(s)
- Yapeng Su
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wei
- NanoSystems Biology Cancer Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.,Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA
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30
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de Oliveira RAG, Materon EM, Melendez ME, Carvalho AL, Faria RC. Disposable Microfluidic Immunoarray Device for Sensitive Breast Cancer Biomarker Detection. ACS APPLIED MATERIALS & INTERFACES 2017; 9:27433-27440. [PMID: 28742317 DOI: 10.1021/acsami.7b03350] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Breast cancer is the most common cancer in women worldwide. The detection of biomarkers has played a significant role in the early diagnosis and prognosis of breast cancer. Herein, we describe the construction of a disposable microfluidic immunoarray device (DμID) for the rapid and low-cost detection of CA15-3 (carbohydrate antigen 15-3), a protein biomarker for breast cancer. The DμID was constructed using a simple and rapid prototyping technique and was applied to detect CA15-3 in cancer patients. The DμID construction was based on the use of a double-sided adhesive card with a microfluidic channel and a screen-printed array with 8 electrodes. Both the immunoarray and microfluidic channel were designed using an inexpensive home cutter printer and using low-cost materials. The immunoarray was modified using the layer-by-layer technique aiming at immobilizing the primary antibody. For the biomarker detection, magnetic particles (MPs) modified with polyclonal antibodies and peroxidase enzymes were used as a strategy for capture, separation, and preconcentration of the biomarker, in addition to amplification of the electroanalytical signal. The preconcentration and amplification strategies integrated with the nanostructured immunosensors of the DμID meaningfully contributed toward the detection of CA15-3 with a limit of detection (LoD) of 6 μU mL-1, requiring as low as 2 μL of serum samples for 8 simultaneous detections. The obtained LoD was 1200 times lower compared to those of other immunosensors previously reported in the literature. The DμID was applied for the detection of CA15-3 in real samples of breast cancer patients and was found to present an excellent correlation with the well-established commercial electrochemiluminescence immunoassay. The association of the DμID with nanostructured surfaces and analyte capturing with bioconjugated paramagnetic particles is essentially a promising breakthrough for the low-cost and accurate detection of cancer biomarkers.
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Affiliation(s)
- Ricardo A G de Oliveira
- Department of Chemistry, Federal University of São Carlos , São Carlos, 13565-905 São Paulo, Brazil
| | - Elsa M Materon
- Department of Chemistry, Federal University of São Carlos , São Carlos, 13565-905 São Paulo, Brazil
| | - Matias E Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital , Barretos, 14784-400 São Paulo, Brazil
| | - André L Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital , Barretos, 14784-400 São Paulo, Brazil
| | - Ronaldo C Faria
- Department of Chemistry, Federal University of São Carlos , São Carlos, 13565-905 São Paulo, Brazil
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31
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Chen Q, Chen YC, Zhang Z, Wu B, Coleman R, Fan X. An integrated microwell array platform for cell lasing analysis. LAB ON A CHIP 2017; 17:2814-2820. [PMID: 28714506 DOI: 10.1039/c7lc00539c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Biological cell lasers are emerging as a novel technology in biological studies and biomedical engineering. The heterogeneity of cells, however, can result in various lasing behaviors from cell to cell. Thus, the capability to track individual cells during laser investigation is highly desired. In this work, a microwell array was integrated with high-quality Fabry-Pérot cavities for addressable and automated cell laser studies. Cells were captured in the microwells and the corresponding cell lasing was achieved and analyzed using SYTO9-stained Sf9 cells as a model system. It is found that the presence of the microwells does not affect the lasing performance, but the cell lasers exhibit strong heterogeneity due to different cell sizes, cycle stages and polyploidy. Time series laser measurements were also performed automatically with the integrated microarray, which not only enables the tracking and multiplexed detection of individual cells, but also helps identify "abnormal" cells that deviate from a large normal cell population in their lasing performance. The microarrayed cell laser platform developed here could provide a powerful tool in single cell analysis using lasing emission that complements conventional fluorescence-based cell analysis.
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Affiliation(s)
- Qiushu Chen
- Department of Biomedical Engineering, University of Michigan, 1101 Beal Avenue, Ann Arbor, Michigan 48109, USA.
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32
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Yu Z, Zhou L, Zhang T, Shen R, Li C, Fang X, Griffiths G, Liu J. Sensitive Detection of MMP9 Enzymatic Activities in Single Cell-Encapsulated Microdroplets as an Assay of Cancer Cell Invasiveness. ACS Sens 2017; 2:626-634. [PMID: 28723167 DOI: 10.1021/acssensors.6b00731] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Matrix metalloproteinases (MMPs) are typically up-regulated in cancer cells, and play a critical role in assisting metastasis by the breakdown of the extracellular matrix. Here we report an effective strategy for cell invasiveness assay by integrating MMP9 functional activity analysis with single cell-encapsulated microdroplets. A flow focusing capillary microfluidic device has been assembled using "off-the-shelf" fluidic components for high-throughput generation of microdroplets. Tumor cells, MMP9 specific peptides, and other cofactors can be loaded into the device and encapsulated into individual droplets as dynamic microreactors for proteolytic cleavage of the substrate. This design allows for rapid and robust detection of MMP9 enzymatic activities by fluorescent signals in a few minutes. It represents the first demonstration of quantifying MMP9 enzymatic activities at the single cell level with a high throughput performance. This new technique promises functional evaluation of cancer cell invasiveness for important diagnostic or prognostic applications.
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Affiliation(s)
- Zhao Yu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Lu Zhou
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Ting Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Rui Shen
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Chenxi Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Xu Fang
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
| | - Gareth Griffiths
- Imagen Therapeutics Ltd, Suite
4D Citylabs, Nelson Street, Manchester M13 9NQ, United Kingdom
| | - Jian Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu Province 215123, China
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Abstract
A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist’s toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays. Digital enzyme assays measure the kinetics of single proteins with enzymatic activity. Digital enzyme-linked immunoassays (ELISAs) quantify antigenic proteins with 2 to 3 log lower detection limit than conventional ELISA, making them well suited for low-abundance biomarkers. Digital cell assays probe single-cell genotype and phenotype, including gene expression, intracellular and surface proteins, metabolic activity, cytotoxicity, and transcriptomes (scRNA-seq). These methods exploit partitioning to 1) isolate single cells or proteins, 2) detect their activity via enzymatic amplification, and 3) tag them individually by coencapsulating them with molecular barcodes. When scaled, digital assays reveal stochastic differences between proteins or cells within a population, a key to understanding biological heterogeneity. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows.
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Affiliation(s)
- Amar S. Basu
- Department of Electrical and Computer Engineering, and Department of Biomedical Engineering, Wayne State University, Detroit, MI, USA
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34
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Lu Y, Yang L, Wei W, Shi Q. Microchip-based single-cell functional proteomics for biomedical applications. LAB ON A CHIP 2017; 17:1250-1263. [PMID: 28280819 PMCID: PMC5459479 DOI: 10.1039/c7lc00037e] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that traditional population-based methods fail to address. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical frameworks to extract new biology. In this review article, we highlight a few biological and clinical applications in which microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating a well-controlled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies.
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Affiliation(s)
- Yao Lu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA. and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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35
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Yang L, Wang Z, Deng Y, Li Y, Wei W, Shi Q. Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray. Anal Chem 2016; 88:11077-11083. [PMID: 27644430 PMCID: PMC5519775 DOI: 10.1021/acs.analchem.6b03086] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circulating tumor cells (CTCs) shed from tumor sites and represent the molecular characteristics of the tumor. Besides genetic and transcriptional characterization, it is important to profile a panel of proteins with single-cell precision for resolving CTCs' phenotype, organ-of-origin, and drug targets. We describe a new technology that enables profiling multiple protein markers of extraordinarily rare tumor cells at the single-cell level. This technology integrates a microchip consisting of 15000 60 pL-sized microwells and a novel beads-on-barcode antibody microarray (BOBarray). The BOBarray allows for multiplexed protein detection by assigning two independent identifiers (bead size and fluorescent color) of the beads to each protein. Four bead sizes (1.75, 3, 4.5, and 6 μm) and three colors (blue, green, and yellow) are utilized to encode up to 12 different proteins. The miniaturized BOBarray can fit an array of 60 pL-sized microwells that isolate single cells for cell lysis and the subsequent detection of protein markers. An enclosed 60 pL-sized microchamber defines a high concentration of proteins released from lysed single cells, leading to single-cell resolution of protein detection. The protein markers assayed in this study include organ-specific markers and drug targets that help to characterize the organ-of-origin and drug targets of isolated rare tumor cells from blood samples. This new approach enables handling a very small number of cells and achieves single-cell, multiplexed protein detection without loss of rare but clinically important tumor cells.
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Affiliation(s)
- Liu Yang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Zhihua Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yuliang Deng
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Li
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Wei Wei
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States
| | - Qihui Shi
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Abstract
Over the last decade, femtoliter arrays have been used as a simple and robust way to encapsulate and monitor the kinetics of single enzyme molecules. Encapsulating individual enzyme molecules within a femtoliter-sized reaction chamber does not require immobilization of the enzyme molecules or fluorescent tagging of the enzyme molecules, which offers the unique advantage of observing unmodified single enzyme molecules free in solution. Several fascinating details about enzyme kinetics have been revealed using these femtoliter arrays, which were unattainable from traditional ensemble experiments. Here, we discuss various considerations to take into account when developing single-molecule enzyme assays in femtoliter arrays and the advantages and disadvantages of various protocols.
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Affiliation(s)
| | - D R Walt
- Tufts University, Medford, MA, United States.
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