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Ho V, Baker JR, Willison KR, Barnes PJ, Donnelly LE, Klug DR. Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells. Commun Biol 2023; 6:458. [PMID: 37100999 PMCID: PMC10133449 DOI: 10.1038/s42003-023-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 04/17/2023] [Indexed: 04/28/2023] Open
Abstract
Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3+ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.
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Affiliation(s)
- Vanessa Ho
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Jonathan R Baker
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Keith R Willison
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
| | - Peter J Barnes
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK
| | - Louise E Donnelly
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Dovehouse Street, London, SW3 6LY, UK.
| | - David R Klug
- Institute of Chemical Biology, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 82 Wood Lane, White City, London, W12 0BZ, UK
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2
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Meyfour A, Pahlavan S, Mirzaei M, Krijgsveld J, Baharvand H, Salekdeh GH. The quest of cell surface markers for stem cell therapy. Cell Mol Life Sci 2021; 78:469-495. [PMID: 32710154 PMCID: PMC11073434 DOI: 10.1007/s00018-020-03602-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/15/2022]
Abstract
Stem cells and their derivatives are novel pharmaceutics that have the potential for use as tissue replacement therapies. However, the heterogeneous characteristics of stem cell cultures have hindered their biomedical applications. In theory and practice, when cell type-specific or stage-specific cell surface proteins are targeted by unique antibodies, they become highly efficient in detecting and isolating specific cell populations. There is a growing demand to identify reliable and actionable cell surface markers that facilitate purification of particular cell types at specific developmental stages for use in research and clinical applications. The identification of these markers as very important members of plasma membrane proteins, ion channels, transporters, and signaling molecules has directly benefited from proteomics and tools for proteomics-derived data analyses. Here, we review the methodologies that have played a role in the discovery of cell surface markers and introduce cutting edge single cell proteomics as an advanced tool. We also discuss currently available specific cell surface markers for stem cells and their lineages, with emphasis on the nervous system, heart, pancreas, and liver. The remaining gaps that pertain to the discovery of these markers and how single cell proteomics and identification of surface markers associated with the progenitor stages of certain terminally differentiated cells may pave the way for their use in regenerative medicine are also discussed.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, Heidelberg, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 672, Heidelberg, Germany
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Banihashem St, P.O. Box: 16635-148, 1665659911, Tehran, Iran.
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3
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Martin K, Zhang T, Zhang P, Chrisler WB, Thomas FL, Liu F, Liu T, Qian WJ, Smith RD, Shi T. Carrier-assisted One-pot Sample Preparation for Targeted Proteomics Analysis of Small Numbers of Human Cells. J Vis Exp 2020:10.3791/61797. [PMID: 33226031 PMCID: PMC8349108 DOI: 10.3791/61797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Protein analysis of small numbers of human cells is primarily achieved by targeted proteomics with antibody-based immunoassays, which have inherent limitations (e.g., low multiplex and unavailability of antibodies for new proteins). Mass spectrometry (MS)-based targeted proteomics has emerged as an alternative because it is antibody-free, high multiplex, and has high specificity and quantitation accuracy. Recent advances in MS instrumentation make MS-based targeted proteomics possible for multiplexed quantification of highly abundant proteins in single cells. However, there is a technical challenge for effective processing of single cells with minimal sample loss for MS analysis. To address this issue, we have recently developed a convenient protein carrier-assisted one-pot sample preparation coupled with liquid chromatography (LC) - selected reaction monitoring (SRM) termed cLC-SRM for targeted proteomics analysis of small numbers of human cells. This method capitalizes on using the combined excessive exogenous protein as a carrier and low-volume one-pot processing to greatly reduce surface adsorption losses as well as high-specificity LC-SRM to effectively address the increased dynamic concentration range due to the addition of exogeneous carrier protein. Its utility has been demonstrated by accurate quantification of most moderately abundant proteins in small numbers of cells (e.g., 10-100 cells) and highly abundant proteins in single cells. The easy-to-implement features and no need for specific devices make this method readily accessible to most proteomics laboratories. Herein we have provided a detailed protocol for cLC-SRM analysis of small numbers of human cells including cell sorting, cell lysis and digestion, LC-SRM analysis, and data analysis. Further improvements in detection sensitivity and sample throughput are needed towards targeted single-cell proteomics analysis. We anticipate that cLC-SRM will be broadly applied to biomedical research and systems biology with the potential of facilitating precision medicine.
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Affiliation(s)
- Kendall Martin
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Pengfei Zhang
- NHC Key Laboratory of Cancer Proteomics, Department of Oncology, Xiangya Hospital, Central South University
| | | | - Fillmore L Thomas
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory
| | - Fen Liu
- Department of Critical Care Medicine, The First Affiliated Hospital of Nanchang University
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory;
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4
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Alam MK, Koomson E, Zou H, Yi C, Li CW, Xu T, Yang M. Recent advances in microfluidic technology for manipulation and analysis of biological cells (2007–2017). Anal Chim Acta 2018; 1044:29-65. [DOI: 10.1016/j.aca.2018.06.054] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/19/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022]
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5
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Manohar S, Shah P, Biswas S, Mukadam A, Joshi M, Viswanathan G. Combining fluorescent cell barcoding and flow cytometry‐based phospho‐ERK1/2 detection at short time scales in adherent cells. Cytometry A 2018; 95:192-200. [DOI: 10.1002/cyto.a.23602] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/09/2018] [Accepted: 08/20/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Sonal Manohar
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Prachi Shah
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Sharmila Biswas
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Anam Mukadam
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Madhura Joshi
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
| | - Ganesh Viswanathan
- Department of Chemical EngineeringIndian Institute of Technology Bombay Powai, Mumbai 400076 India
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6
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Chatzimichail S, Supramaniam P, Ces O, Salehi-Reyhani A. Counting Proteins in Single Cells with Addressable Droplet Microarrays. J Vis Exp 2018. [PMID: 30035757 DOI: 10.3791/56110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Often cellular behavior and cellular responses are analyzed at the population level where the responses of many cells are pooled together as an average result masking the rich single cell behavior within a complex population. Single cell protein detection and quantification technologies have made a remarkable impact in recent years. Here we describe a practical and flexible single cell analysis platform based on addressable droplet microarrays. This study describes how the absolute copy numbers of target proteins may be measured with single cell resolution. The tumor suppressor p53 is the most commonly mutated gene in human cancer, with more than 50% of total cancer cases exhibiting a non-healthy p53 expression pattern. The protocol describes steps to create 10 nL droplets within which single human cancer cells are isolated and the copy number of p53 protein is measured with single molecule resolution to precisely determine the variability in expression. The method may be applied to any cell type including primary material to determine the absolute copy number of any target proteins of interest.
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Affiliation(s)
| | | | - Oscar Ces
- Institute of Chemical Biology, Department of Chemistry, Imperial College London
| | - Ali Salehi-Reyhani
- Institute of Chemical Biology, Department of Chemistry, Imperial College London;
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7
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Gong H, Wang X, Liu B, Boutet S, Holcomb I, Dakshinamoorthy G, Ooi A, Sanada C, Sun G, Ramakrishnan R. Single-cell protein-mRNA correlation analysis enabled by multiplexed dual-analyte co-detection. Sci Rep 2017; 7:2776. [PMID: 28584233 PMCID: PMC5459813 DOI: 10.1038/s41598-017-03057-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/24/2017] [Indexed: 01/01/2023] Open
Abstract
We have investigated the correlation between proteins and mRNAs in single cells employing an integrated workflow for dual-analyte co-detection. This is achieved by combining the oligo extension reaction (OER), which converts protein levels to DNA levels, with reverse transcription for mRNA detection. Unsupervised gene expression profiling analysis, including principal component analysis and hierarchical clustering, revealed different aspects of the protein-mRNA relationship. Violin plot analysis showed that some genes exhibited similar distribution patterns for proteins and mRNAs. We also demonstrate that cells can be separated into subpopulations based on their protein-mRNA expression profiles, and that different subpopulations have distinct correlation coefficient values. Our results demonstrated that integrated investigations of mRNA and protein levels in single cells allows comprehensive analysis not attainable at bulk levels.
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Affiliation(s)
- Haibiao Gong
- Fluidigm Corporation, South San Francisco, CA, 94080, USA.
| | - Xiaohui Wang
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Benjamin Liu
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | | | - Ilona Holcomb
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | | | - Aik Ooi
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Chad Sanada
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
| | - Gang Sun
- Fluidigm Corporation, South San Francisco, CA, 94080, USA
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8
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Magness AJ, Squires JA, Griffiths B, Khan K, Swain A, Willison KR, Cunningham D, Gerlinger M, Klug DR. Multiplexed single cell protein expression analysis in solid tumours using a miniaturised microfluidic assay. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa6aae] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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9
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Preston GM. Profiling the extended phenotype of plant pathogens: Challenges in Bacterial Molecular Plant Pathology. MOLECULAR PLANT PATHOLOGY 2017; 18:443-456. [PMID: 28026146 PMCID: PMC6638297 DOI: 10.1111/mpp.12530] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/18/2023]
Abstract
One of the most fundamental questions in plant pathology is what determines whether a pathogen grows within a plant? This question is frequently studied in terms of the role of elicitors and pathogenicity factors in the triggering or overcoming of host defences. However, this focus fails to address the basic question of how the environment in host tissues acts to support or restrict pathogen growth. Efforts to understand this aspect of host-pathogen interactions are commonly confounded by several issues, including the complexity of the plant environment, the artificial nature of many experimental infection systems and the fact that the physiological properties of a pathogen growing in association with a plant can be very different from the properties of the pathogen in culture. It is also important to recognize that the phenotype and evolution of pathogen and host are inextricably linked through their interactions, such that the environment experienced by a pathogen within a host, and its phenotype within the host, is a product of both its interaction with its host and its evolutionary history, including its co-evolution with host plants. As the phenotypic properties of a pathogen within a host cannot be defined in isolation from the host, it may be appropriate to think of pathogens as having an 'extended phenotype' that is the product of their genotype, host interactions and population structure within the host environment. This article reflects on the challenge of defining and studying this extended phenotype, in relation to the questions posed below, and considers how knowledge of the phenotype of pathogens in the host environment could be used to improve disease control. What determines whether a pathogen grows within a plant? What aspects of pathogen biology should be considered in describing the extended phenotype of a pathogen within a host? How can we study the extended phenotype in ways that provide insights into the phenotypic properties of pathogens during natural infections?
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Affiliation(s)
- Gail M. Preston
- Department of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
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10
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Chaudhuri PK, Ebrahimi Warkiani M, Jing T, Kenry, Lim CT. Microfluidics for research and applications in oncology. Analyst 2017; 141:504-24. [PMID: 26010996 DOI: 10.1039/c5an00382b] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cancer is currently one of the top non-communicable human diseases, and continual research and developmental efforts are being made to better understand and manage this disease. More recently, with the improved understanding in cancer biology as well as the advancements made in microtechnology and rapid prototyping, microfluidics is increasingly being explored and even validated for use in the detection, diagnosis and treatment of cancer. With inherent advantages such as small sample volume, high sensitivity and fast processing time, microfluidics is well-positioned to serve as a promising platform for applications in oncology. In this review, we look at the recent advances in the use of microfluidics, from basic research such as understanding cancer cell phenotypes as well as metastatic behaviors to applications such as the detection, diagnosis, prognosis and drug screening. We then conclude with a future outlook on this promising technology.
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Affiliation(s)
| | - Majid Ebrahimi Warkiani
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602 and School of Mechanical and Manufacturing Engineering, Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Tengyang Jing
- BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602 and Department of Biomedical Engineering, National University of Singapore, Singapore 117575.
| | - Kenry
- Department of Biomedical Engineering, National University of Singapore, Singapore 117575. and NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Chwee Teck Lim
- Mechanobiology Institute, National University of Singapore, Singapore 117411 and BioSystems and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore 138602
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11
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Gavasso S, Gullaksen SE, Skavland J, Gjertsen BT. Single-cell proteomics: potential implications for cancer diagnostics. Expert Rev Mol Diagn 2016; 16:579-89. [DOI: 10.1586/14737159.2016.1156531] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sonia Gavasso
- Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | | | - Jørn Skavland
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Bjørn T. Gjertsen
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Translational Hemato-Oncology Group, University of Bergen, Bergen, Norway
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12
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Sánchez-Ovejero C, Benito-Lopez F, Díez P, Casulli A, Siles-Lucas M, Fuentes M, Manzano-Román R. Sensing parasites: Proteomic and advanced bio-detection alternatives. J Proteomics 2016; 136:145-56. [PMID: 26773860 DOI: 10.1016/j.jprot.2015.12.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 12/12/2022]
Abstract
Parasitic diseases have a great impact in human and animal health. The gold standard for the diagnosis of the majority of parasitic infections is still conventional microscopy, which presents important limitations in terms of sensitivity and specificity and commonly requires highly trained technicians. More accurate molecular-based diagnostic tools are needed for the implementation of early detection, effective treatments and massive screenings with high-throughput capacities. In this respect, sensitive and affordable devices could greatly impact on sustainable control programmes which exist against parasitic diseases, especially in low income settings. Proteomics and nanotechnology approaches are valuable tools for sensing pathogens and host alteration signatures within microfluidic detection platforms. These new devices might provide novel solutions to fight parasitic diseases. Newly described specific parasite derived products with immune-modulatory properties have been postulated as the best candidates for the early and accurate detection of parasitic infections as well as for the blockage of parasite development. This review provides the most recent methodological and technological advances with great potential for bio-sensing parasites in their hosts, showing the newest opportunities offered by modern "-omics" and platforms for parasite detection and control.
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Affiliation(s)
- Carlos Sánchez-Ovejero
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Fernando Benito-Lopez
- Analytical Chemistry Department, Universidad del País Vasco UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Adriano Casulli
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, - 00161 Rome, Italy
| | - Mar Siles-Lucas
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain.
| | - Raúl Manzano-Román
- Instituto de Recursos Naturales y Agrobiología de Salamanca (IRNASA-CSIC), 37008 Salamanca, Spain.
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13
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Gong H, Holcomb I, Ooi A, Wang X, Majonis D, Unger MA, Ramakrishnan R. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells. Bioconjug Chem 2016; 27:217-25. [PMID: 26689321 DOI: 10.1021/acs.bioconjchem.5b00613] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and is well-suited for the development of affordable multiplex protein assays, which provides the potential to accelerate proteomics research.
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Affiliation(s)
- Haibiao Gong
- Fluidigm Corporation , South San Francisco, California 94080, United States
| | - Ilona Holcomb
- Fluidigm Corporation , South San Francisco, California 94080, United States
| | - Aik Ooi
- Fluidigm Corporation , South San Francisco, California 94080, United States
| | - Xiaohui Wang
- Fluidigm Corporation , South San Francisco, California 94080, United States
| | - Daniel Majonis
- Fluidigm Corporation , South San Francisco, California 94080, United States
| | - Marc A Unger
- Fluidigm Corporation , South San Francisco, California 94080, United States
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14
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Abstract
Protein phosphorylation is a ubiquitous posttranslational modification, which is heavily involved in signal transduction. Misregulation of protein phosphorylation is often associated with a decrease in cell viability and complex diseases such as cancer. The dynamic and low abundant nature of phosphorylated proteins makes studying phosphoproteome a challenging task. In this review, we summarize state of the art proteomic techniques to study and quantify peptide phosphorylation in biological systems and discuss their limitations. Due to its short-lived nature, the phosphorylation event cannot be precisely traced in a heterogonous cell population, which highlights the importance of analyzing phosphorylation events at the single cell level. Mainly, we focus on the methodical and instrumental developments in proteomics and nanotechnology, which will help to build more accurate and robust systems for the feasibility of phosphorylation analysis at the single cell level. We propose that an automated and miniaturized construction of analytical systems holds the key to the future of phosphoproteomics; therefore, we highlight the benchmark studies in this direction. Having advanced and automated microfluidic chip LC systems will allow us to analyze single-cell phosphoproteomics and quantitatively compare it with others. The progress in the microfluidic chip LC systems and feasibility of the single-cell phosphoproteomics will be beneficial for early diagnosis and detection of the treatment response of many crucial diseases.
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Affiliation(s)
- Ayse Nur Polat
- Department of Molecular Biology and Genetics, Science Faculty, Koç University, Istanbul, Turkey.
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15
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Kunert KJ, van Wyk SG, Cullis CA, Vorster BJ, Foyer CH. Potential use of phytocystatins in crop improvement, with a particular focus on legumes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3559-70. [PMID: 25944929 DOI: 10.1093/jxb/erv211] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Phytocystatins are a well-characterized class of naturally occurring protease inhibitors that function by preventing the catalysis of papain-like cysteine proteases. The action of cystatins in biotic stress resistance has been studied intensively, but relatively little is known about their functions in plant growth and defence responses to abiotic stresses, such as drought. Extreme weather events, such as drought and flooding, will have negative impacts on the yields of crop plants, particularly grain legumes. The concepts that changes in cellular protein content and composition are required for acclimation to different abiotic stresses, and that these adjustments are achieved through regulation of proteolysis, are widely accepted. However, the nature and regulation of the protein turnover machinery that underpins essential stress-induced cellular restructuring remain poorly characterized. Cysteine proteases are intrinsic to the genetic programmes that underpin plant development and senescence, but their functions in stress-induced senescence are not well defined. Transgenic plants including soybean that have been engineered to constitutively express phytocystatins show enhanced tolerance to a range of different abiotic stresses including drought, suggesting that manipulation of cysteine protease activities by altered phytocystatin expression in crop plants might be used to improve resilience and quality in the face of climate change.
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Affiliation(s)
- Karl J Kunert
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Stefan G van Wyk
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christopher A Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Barend J Vorster
- Department of Plant Production and Soil Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Christine H Foyer
- Centre for Plant Sciences, School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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Recent advances and current issues in single-cell sequencing of tumors. Cancer Lett 2015; 365:1-10. [PMID: 26003306 DOI: 10.1016/j.canlet.2015.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/19/2015] [Accepted: 04/20/2015] [Indexed: 12/28/2022]
Abstract
Intratumoral heterogeneity is a recently recognized but important feature of cancer that underlies the various biocharacteristics of cancer tissues. The advent of next-generation sequencing technologies has facilitated large scale capture of genomic data, while the recent development of single-cell sequencing has allowed for more in-depth studies into the complex molecular mechanisms of intratumoral heterogeneity. In this review, the recent advances and current challenges in single-cell sequencing methodologies are discussed, highlighting the potential power of these data to provide insights into oncological processes, from tumorigenesis through progression to metastasis and therapy resistance.
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Galler K, Bräutigam K, Große C, Popp J, Neugebauer U. Making a big thing of a small cell--recent advances in single cell analysis. Analyst 2015; 139:1237-73. [PMID: 24495980 DOI: 10.1039/c3an01939j] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Single cell analysis is an emerging field requiring a high level interdisciplinary collaboration to provide detailed insights into the complex organisation, function and heterogeneity of life. This review is addressed to life science researchers as well as researchers developing novel technologies. It covers all aspects of the characterisation of single cells (with a special focus on mammalian cells) from morphology to genetics and different omics-techniques to physiological, mechanical and electrical methods. In recent years, tremendous advances have been achieved in all fields of single cell analysis: (1) improved spatial and temporal resolution of imaging techniques to enable the tracking of single molecule dynamics within single cells; (2) increased throughput to reveal unexpected heterogeneity between different individual cells raising the question what characterizes a cell type and what is just natural biological variation; and (3) emerging multimodal approaches trying to bring together information from complementary techniques paving the way for a deeper understanding of the complexity of biological processes. This review also covers the first successful translations of single cell analysis methods to diagnostic applications in the field of tumour research (especially circulating tumour cells), regenerative medicine, drug discovery and immunology.
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Affiliation(s)
- Kerstin Galler
- Integrated Research and Treatment Center "Center for Sepsis Control and Care", Jena University Hospital, Erlanger Allee 101, 07747 Jena, Germany
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Subramanian N, Torabi-Parizi P, Gottschalk RA, Germain RN, Dutta B. Network representations of immune system complexity. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2015; 7:13-38. [PMID: 25625853 PMCID: PMC4339634 DOI: 10.1002/wsbm.1288] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 12/09/2014] [Accepted: 12/11/2014] [Indexed: 12/25/2022]
Abstract
The mammalian immune system is a dynamic multiscale system composed of a hierarchically organized set of molecular, cellular, and organismal networks that act in concert to promote effective host defense. These networks range from those involving gene regulatory and protein–protein interactions underlying intracellular signaling pathways and single‐cell responses to increasingly complex networks of in vivo cellular interaction, positioning, and migration that determine the overall immune response of an organism. Immunity is thus not the product of simple signaling events but rather nonlinear behaviors arising from dynamic, feedback‐regulated interactions among many components. One of the major goals of systems immunology is to quantitatively measure these complex multiscale spatial and temporal interactions, permitting development of computational models that can be used to predict responses to perturbation. Recent technological advances permit collection of comprehensive datasets at multiple molecular and cellular levels, while advances in network biology support representation of the relationships of components at each level as physical or functional interaction networks. The latter facilitate effective visualization of patterns and recognition of emergent properties arising from the many interactions of genes, molecules, and cells of the immune system. We illustrate the power of integrating ‘omics’ and network modeling approaches for unbiased reconstruction of signaling and transcriptional networks with a focus on applications involving the innate immune system. We further discuss future possibilities for reconstruction of increasingly complex cellular‐ and organism‐level networks and development of sophisticated computational tools for prediction of emergent immune behavior arising from the concerted action of these networks. WIREs Syst Biol Med 2015, 7:13–38. doi: 10.1002/wsbm.1288 This article is categorized under:
Analytical and Computational Methods > Computational Methods Laboratory Methods and Technologies > Macromolecular Interactions, Methods
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Affiliation(s)
- Naeha Subramanian
- Institute for Systems Biology, Seattle, WA, USA; Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Abstract
Single-cell analysis heralds a new era that allows “omics” analysis, notably genomics, transcriptomics, epigenomics and proteomics at the single-cell level. It enables the identification of the minor subpopulations that may play a critical role in a biological process of a population of cells, which conventionally are regarded as homogeneous. It provides an ultra-sensitive tool to clarify specific molecular mechanisms and pathways and reveal the nature of cell heterogeneity. It also facilitates the clinical investigation of patients when a very low quantity or a single cell is available for analysis, such as noninvasive prenatal diagnosis and cancer screening, and genetic evaluation for in vitro fertilization. Within a few short years, single-cell analysis, especially whole genomic sequencing and transcriptomic sequencing, is becoming robust and broadly accessible, although not yet a routine practice. Here, with single cell RNA-seq emphasized, an overview of the discipline, progresses, and prospects of single-cell analysis and its applications in biology and medicine are given with a series of logic and theoretical considerations.
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Affiliation(s)
- Xinghua Pan
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
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20
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Etzrodt M, Endele M, Schroeder T. Quantitative single-cell approaches to stem cell research. Cell Stem Cell 2014; 15:546-58. [PMID: 25517464 DOI: 10.1016/j.stem.2014.10.015] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding the molecular control of cell fates is central to stem cell research. Such insight requires quantification of molecular and cellular behavior at the single-cell level. Recent advances now permit high-throughput molecular readouts from single cells as well as continuous, noninvasive observation of cell behavior over time. Here, we review current state-of-the-art approaches used to query stem cell fate at the single-cell level, including advances in lineage tracing, time-lapse imaging, and molecular profiling. We also offer our perspective on the advantages and drawbacks of available approaches, key technical limitations, considerations for data interpretation, and future innovation.
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Affiliation(s)
- Martin Etzrodt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Max Endele
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
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Salehi-Reyhani A, Burgin E, Ces O, Willison KR, Klug DR. Addressable droplet microarrays for single cell protein analysis. Analyst 2014; 139:5367-74. [DOI: 10.1039/c4an01208a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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22
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Shao Y, Fu J. Integrated micro/nanoengineered functional biomaterials for cell mechanics and mechanobiology: a materials perspective. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:1494-533. [PMID: 24339188 PMCID: PMC4076293 DOI: 10.1002/adma.201304431] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 10/11/2013] [Indexed: 04/14/2023]
Abstract
The rapid development of micro/nanoengineered functional biomaterials in the last two decades has empowered materials scientists and bioengineers to precisely control different aspects of the in vitro cell microenvironment. Following a philosophy of reductionism, many studies using synthetic functional biomaterials have revealed instructive roles of individual extracellular biophysical and biochemical cues in regulating cellular behaviors. Development of integrated micro/nanoengineered functional biomaterials to study complex and emergent biological phenomena has also thrived rapidly in recent years, revealing adaptive and integrated cellular behaviors closely relevant to human physiological and pathological conditions. Working at the interface between materials science and engineering, biology, and medicine, we are now at the beginning of a great exploration using micro/nanoengineered functional biomaterials for both fundamental biology study and clinical and biomedical applications such as regenerative medicine and drug screening. In this review, an overview of state of the art micro/nanoengineered functional biomaterials that can control precisely individual aspects of cell-microenvironment interactions is presented and they are highlighted them as well-controlled platforms for mechanistic studies of mechano-sensitive and -responsive cellular behaviors and integrative biology research. The recent exciting trend where micro/nanoengineered biomaterials are integrated into miniaturized biological and biomimetic systems for dynamic multiparametric microenvironmental control of emergent and integrated cellular behaviors is also discussed. The impact of integrated micro/nanoengineered functional biomaterials for future in vitro studies of regenerative medicine, cell biology, as well as human development and disease models are discussed.
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Affiliation(s)
- Yue Shao
- Integrated Biosystems and Biomechanics Laboratory, Department of Mechanical Engineering, University of Michigan, Ann Arbor, 48109 (USA)
| | - Jianping Fu
- Integrated Biosystems and Biomechanics Laboratory, Department of Mechanical Engineering, University of Michigan, Ann Arbor, 48109 (USA). Department of Biomedical Engineering, University of Michigan, Ann Arbor, 48109 (USA)
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23
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Burgin E, Salehi-Reyhani A, Barclay M, Brown A, Kaplinsky J, Novakova M, Neil MAA, Ces O, Willison KR, Klug DR. Absolute quantification of protein copy number using a single-molecule-sensitive microarray. Analyst 2014; 139:3235-44. [DOI: 10.1039/c4an00091a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Abstract
We all start out as a single totipotent cell that is programmed to produce a multicellular organism. How do individual cells make those complex developmental switches? How do single cells within a tissue or organ differ, how do they coordinate their actions or go astray in a disease process? These are long-standing and fundamental questions in biology that are now becoming tractable because of advances in microfluidics, DNA amplification and DNA sequencing. Methods for studying single-cell transcriptomes (or at least the polyadenylated mRNA fraction of it) are by far the furthest ahead and reveal remarkable heterogeneity between morphologically identical cells. The analysis of genomic DNA variation is not far behind. The other 'omics' of single cells pose greater technological obstacles, but they are progressing and promise to yield highly integrated large data sets in the near future.
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