251
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Stand-Sit Microchip for High-Throughput, Multiplexed Analysis of Single Cancer Cells. Sci Rep 2016; 6:32505. [PMID: 27581736 PMCID: PMC5007481 DOI: 10.1038/srep32505] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/10/2016] [Indexed: 12/15/2022] Open
Abstract
Cellular heterogeneity in function and response to therapeutics has been a major challenge in cancer treatment. The complex nature of tumor systems calls for the development of advanced multiplexed single-cell tools that can address the heterogeneity issue. However, to date such tools are only available in a laboratory setting and don’t have the portability to meet the needs in point-of-care cancer diagnostics. Towards that application, we have developed a portable single-cell system that is comprised of a microchip and an adjustable clamp, so on-chip operation only needs pipetting and adjusting of clamping force. Up to 10 proteins can be quantitated from each cell with hundreds of single-cell assays performed in parallel from one chip operation. We validated the technology and analyzed the oncogenic signatures of cancer stem cells by quantitating both aldehyde dehydrogenase (ALDH) activities and 5 signaling proteins in single MDA-MB-231 breast cancer cells. The technology has also been used to investigate the PI3K pathway activities of brain cancer cells expressing mutant epidermal growth factor receptor (EGFR) after drug intervention targeting EGFR signaling. Our portable single-cell system will potentially have broad application in the preclinical and clinical settings for cancer diagnosis in the future.
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252
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Stumpf PS, Ewing R, MacArthur BD. Single-cell pluripotency regulatory networks. Proteomics 2016; 16:2303-12. [PMID: 27357612 DOI: 10.1002/pmic.201500528] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/21/2016] [Accepted: 06/27/2016] [Indexed: 11/09/2022]
Abstract
Pluripotent stem cells (PSCs) are a popular model system for investigating development, tissue regeneration, and repair. Although much is known about the molecular mechanisms that regulate the balance between self-renewal and lineage commitment in PSCs, the spatiotemporal integration of responsive signaling pathways with core transcriptional regulatory networks are complex and only partially understood. Moreover, measurements made on populations of cells reveal only average properties of the underlying regulatory networks, obscuring their fine detail. Here, we discuss the reconstruction of regulatory networks in individual cells using novel single-cell transcriptomics and proteomics, in order to expand our understanding of the molecular basis of pluripotency, including the role of cell-cell variability within PSC populations, and ways in which networks may be controlled in order to reliably manipulate cell behavior.
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Affiliation(s)
- Patrick S Stumpf
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rob Ewing
- Institute for Life Sciences, University of Southampton, Southampton, UK.,Centre for Biological Sciences, University of Southampton, Southampton, UK
| | - Ben D MacArthur
- Centre for Human Development, Stem Cells and Regeneration, University of Southampton, Southampton, UK. .,Institute for Life Sciences, University of Southampton, Southampton, UK. .,Department of Mathematics, University of Southampton, Southampton, UK.
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253
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Mainz ER, Serafin DS, Nguyen TT, Tarrant TK, Sims CE, Allbritton NL. Single Cell Chemical Cytometry of Akt Activity in Rheumatoid Arthritis and Normal Fibroblast-like Synoviocytes in Response to Tumor Necrosis Factor α. Anal Chem 2016; 88:7786-92. [PMID: 27391352 PMCID: PMC6040665 DOI: 10.1021/acs.analchem.6b01801] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The etiology of rheumatoid arthritis (RA) is poorly understood, and 30% of patients are unresponsive to established treatments targeting tumor necrosis factor α (TNFα). Akt kinase is implicated in TNFα signaling and may act as a barometer of patient responses to biologic therapies. Fluorescent peptide sensors and chemical cytometry were employed to directly measure Akt activity as well as proteolytic activity in individual fibroblast-like synoviocytes (FLS) from RA and normal subjects. The specificity of the peptide reporter was evaluated and shown to be a valid measure of Akt activity in single cells. The effect of TNFα treatment on Akt activity was highly heterogeneous between normal and RA subjects, which was not observable in bulk analyses. In 2 RA subjects, a bimodal distribution of Akt activity was observed, primarily due to a subpopulation (21.7%: RA Subject 5; 23.8%: RA Subject 6) of cells in which >60% of the reporter was phosphorylated. These subjects also possessed statistically elevated proteolytic cleavage of the reporter relative to normal subjects, suggesting heterogeneity in Akt and protease activity that may play a role in the RA-affected joint. We expect that chemical cytometry studies pairing peptide reporters with capillary electrophoresis will provide valuable data regarding aberrant kinase activity from small samples of clinical interest.
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Affiliation(s)
- Emilie R. Mainz
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - D. Stephen Serafin
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
| | - Tuong T. Nguyen
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Teresa K. Tarrant
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, USA
- Department of Medicine, Division of Rheumatology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, 27599, USA
| | - Christopher E. Sims
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Medicine, Division of Rheumatology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA and North Carolina State University, Raleigh, North Carolina 27695, US
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254
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Abstract
In this issue of Molecular Cell, Tay and colleagues (Albayrak et al., 2016) describe a new technique to digitally quantify the numbers of protein and mRNA in the same mammalian cell, providing a new way to look at the central dogma of molecular biology.
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Affiliation(s)
- Yihan Lin
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering and Department of Applied Physics, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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255
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Digital Quantification of Proteins and mRNA in Single Mammalian Cells. Mol Cell 2016; 61:914-24. [PMID: 26990994 DOI: 10.1016/j.molcel.2016.02.030] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 01/19/2016] [Accepted: 02/25/2016] [Indexed: 01/23/2023]
Abstract
Absolute quantification of macromolecules in single cells is critical for understanding and modeling biological systems that feature cellular heterogeneity. Here we show extremely sensitive and absolute quantification of both proteins and mRNA in single mammalian cells by a very practical workflow that combines proximity ligation assay (PLA) and digital PCR. This digital PLA method has femtomolar sensitivity, which enables the quantification of very small protein concentration changes over its entire 3-log dynamic range, a quality necessary for accounting for single-cell heterogeneity. We counted both endogenous (CD147) and exogenously expressed (GFP-p65) proteins from hundreds of single cells and determined the correlation between CD147 mRNA and the protein it encodes. Using our data, a stochastic two-state model of the central dogma was constructed and verified using joint mRNA/protein distributions, allowing us to estimate transcription burst sizes and extrinsic noise strength and calculate the transcription and translation rate constants in single mammalian cells.
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256
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Day EK, Sosale NG, Lazzara MJ. Cell signaling regulation by protein phosphorylation: a multivariate, heterogeneous, and context-dependent process. Curr Opin Biotechnol 2016; 40:185-192. [PMID: 27393828 PMCID: PMC4975652 DOI: 10.1016/j.copbio.2016.06.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/21/2016] [Accepted: 06/21/2016] [Indexed: 02/08/2023]
Abstract
Proper spatiotemporal regulation of protein phosphorylation in cells and tissues is required for normal development and homeostasis, but aberrant protein phosphorylation regulation leads to various diseases. The study of signaling regulation by protein phosphorylation is complicated in part by the sheer scope of the kinome and phosphoproteome, dependence of signaling protein functionality on cellular localization, and the complex multivariate relationships that exist between protein phosphorylation dynamics and the cellular phenotypes they control. Additional complexities arise from the ability of microenvironmental factors to influence phosphorylation-dependent signaling and from the tendency for some signaling processes to occur heterogeneously among cells. These considerations should be taken into account when measuring cell signaling regulation by protein phosphorylation.
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Affiliation(s)
- Evan K Day
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Nisha G Sosale
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew J Lazzara
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, United States; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, United States.
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257
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Ni D, Xu P, Gallagher S. Immunoblotting and Immunodetection. ACTA ACUST UNITED AC 2016; 114:8.10.1-8.10.36. [DOI: 10.1002/cpim.10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Peng Xu
- Department of Pathology University of Virginia School of Medicine Charlottesville Virginia
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258
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Abstract
INTRODUCTION Cellular heterogeneity has challenged current cancer therapeutics and hindered the discovery and development of cancer drugs. The heterogeneity in functional proteome is of particular interest because many cancer drugs are developed to target signaling proteins. The complex nature of tumor systems calls for more advanced multiplexed single-cell tools to address the heterogeneity issue. AREA COVERED Over the past five years, there are a few single-cell functional proteomics tools introduced with unprecedented multiplexity and performance that are transforming the oncology field. Those tools are generally categorized as cytometry-based tools and microfluidics-based tools, and we discuss the representatives in both categories. Expert commentary: The single-cell tools have provided an avenue to understand the multifaceted differences of cancer cells, the complex signaling networks, and the relationship of intercellular interaction and tumor architecture. We also provide an outlook of single-cell tools in five years and the challenges to address before a greater impact on oncology can be made.
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Affiliation(s)
- Jun Wang
- a Multiplex Biotechnology Laboratory, Department of Chemistry , University at Albany, State University of New York , Albany , NY , USA.,b Cancer Research Center , University at Albany, State University of New York , Rensselaer , NY , USA
| | - Fan Yang
- a Multiplex Biotechnology Laboratory, Department of Chemistry , University at Albany, State University of New York , Albany , NY , USA
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259
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Kang CC, Yamauchi KA, Vlassakis J, Sinkala E, Duncombe TA, Herr AE. Single cell-resolution western blotting. Nat Protoc 2016; 11:1508-30. [PMID: 27466711 DOI: 10.1038/nprot.2016.089] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This protocol describes how to perform western blotting on individual cells to measure cell-to-cell variation in protein expression levels and protein state. Like conventional western blotting, single-cell western blotting (scWB) is particularly useful for protein targets that lack selective antibodies (e.g., isoforms) and in cases in which background signal from intact cells is confounding. scWB is performed on a microdevice that comprises an array of microwells molded in a thin layer of a polyacrylamide gel (PAG). The gel layer functions as both a molecular sieving matrix during PAGE and a blotting scaffold during immunoprobing. scWB involves five main stages: (i) gravity settling of cells into microwells; (ii) chemical lysis of cells in each microwell; (iii) PAGE of each single-cell lysate; (iv) exposure of the gel to UV light to blot (immobilize) proteins to the gel matrix; and (v) in-gel immunoprobing of immobilized proteins. Multiplexing can be achieved by probing with antibody cocktails and using antibody stripping/reprobing techniques, enabling detection of 10+ proteins in each cell. We also describe microdevice fabrication for both uniform and pore-gradient microgels. To extend in-gel immunoprobing to gels of small pore size, we describe an optional gel de-cross-linking protocol for more effective introduction of antibodies into the gel layer. Once the microdevice has been fabricated, the assay can be completed in 4-6 h by microfluidic novices and it generates high-selectivity, multiplexed data from single cells. The technique is relevant when direct measurement of proteins in single cells is needed, with applications spanning the fundamental biosciences to applied biomedicine.
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Affiliation(s)
- Chi-Chih Kang
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Kevin A Yamauchi
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Julea Vlassakis
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Elly Sinkala
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Todd A Duncombe
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
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260
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Coskun AF, Eser U, Islam S. Cellular identity at the single-cell level. MOLECULAR BIOSYSTEMS 2016; 12:2965-79. [PMID: 27460751 DOI: 10.1039/c6mb00388e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.
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Affiliation(s)
- Ahmet F Coskun
- Division of Chemistry and Chemical Engineering, California Institute of Technology, California, USA.
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261
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Doura T, Kamiya M, Obata F, Yamaguchi Y, Hiyama TY, Matsuda T, Fukamizu A, Noda M, Miura M, Urano Y. Detection of LacZ-Positive Cells in Living Tissue with Single-Cell Resolution. Angew Chem Int Ed Engl 2016; 55:9620-4. [PMID: 27400827 DOI: 10.1002/anie.201603328] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Indexed: 11/11/2022]
Abstract
The LacZ gene, which encodes Escherichia coli β-galactosidase, is widely used as a marker for cells with targeted gene expression or disruption. However, it has been difficult to detect lacZ-positive cells in living organisms or tissues at single-cell resolution, limiting the utility of existing lacZ reporters. Herein we present a newly developed fluorogenic β-galactosidase substrate suitable for labeling live cells in culture, as well as in living tissues. This precisely functionalized fluorescent probe exhibited dramatic activation of fluorescence upon reaction with the enzyme, remained inside cells by anchoring itself to intracellular proteins, and provided single-cell resolution. Neurons labeled with this probe preserved spontaneous firing, which was enhanced by application of ligands of receptors expressed in the cells, suggesting that this probe would be applicable to investigate functions of targeted cells in living tissues and organisms.
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Affiliation(s)
- Tomohiro Doura
- Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,PRESTO, Japan, Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Fumiaki Obata
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshifumi Yamaguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,PRESTO, Japan, Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takeshi Y Hiyama
- Division of Molecular Neurobiology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.,School of Life Science, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Takashi Matsuda
- School of Life Science, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance, Tsukuba, Ibaraki, 305-8577, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Masaharu Noda
- Division of Molecular Neurobiology, National Institute for Basic Biology, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.,School of Life Science, The Graduate University for Advanced Studies, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan
| | - Masayuki Miura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,CREST, Japan, Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yasuteru Urano
- Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan. .,CREST, Japan, Agency for Medical Research and Development, 1-7-1 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan.
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262
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Doura T, Kamiya M, Obata F, Yamaguchi Y, Hiyama TY, Matsuda T, Fukamizu A, Noda M, Miura M, Urano Y. Detection ofLacZ-Positive Cells in Living Tissue with Single-Cell Resolution. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603328] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Tomohiro Doura
- Graduate School of Medicine; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Mako Kamiya
- Graduate School of Medicine; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
- PRESTO, Japan, Science and Technology Agency; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Fumiaki Obata
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Yoshifumi Yamaguchi
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- PRESTO, Japan, Science and Technology Agency; 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
| | - Takeshi Y. Hiyama
- Division of Molecular Neurobiology; National Institute for Basic Biology; 5-1 Higashiyama Myodaiji-cho, Okazaki Aichi 444-8787 Japan
- School of Life Science; The Graduate University for Advanced Studies; 5-1 Higashiyama Myodaiji-cho, Okazaki Aichi 444-8787 Japan
| | - Takashi Matsuda
- School of Life Science; The Graduate University for Advanced Studies; 5-1 Higashiyama Myodaiji-cho, Okazaki Aichi 444-8787 Japan
| | - Akiyoshi Fukamizu
- Life Science Center, Tsukuba Advanced Research Alliance; Tsukuba Ibaraki 305-8577 Japan
- Graduate School of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki, 305-8577 Japan
| | - Masaharu Noda
- Division of Molecular Neurobiology; National Institute for Basic Biology; 5-1 Higashiyama Myodaiji-cho, Okazaki Aichi 444-8787 Japan
- School of Life Science; The Graduate University for Advanced Studies; 5-1 Higashiyama Myodaiji-cho, Okazaki Aichi 444-8787 Japan
| | - Masayuki Miura
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- CREST, Japan, Agency for Medical Research and Development; 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
| | - Yasuteru Urano
- Graduate School of Medicine; The University of Tokyo; 7-3-1, Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Graduate School of Pharmaceutical Sciences; The University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- CREST, Japan, Agency for Medical Research and Development; 1-7-1 Otemachi Chiyoda-ku Tokyo 100-0004 Japan
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263
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Chen YC, Cheng YH, Ingram P, Yoon E. Single Cell Proteolytic Assays to Investigate Cancer Clonal Heterogeneity and Cell Dynamics Using an Efficient Cell Loading Scheme. Sci Rep 2016; 6:27154. [PMID: 27283981 PMCID: PMC4901291 DOI: 10.1038/srep27154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/03/2016] [Indexed: 02/07/2023] Open
Abstract
Proteolytic degradation of the extracellular matrix (ECM) is critical in cancer invasion, and recent work suggests that heterogeneous cancer populations cooperate in this process. Despite the importance of cell heterogeneity, conventional proteolytic assays measure average activity, requiring thousands of cells and providing limited information about heterogeneity and dynamics. Here, we developed a microfluidic platform that provides high-efficiency cell loading and simple valveless isolation, so the proteolytic activity of a small sample (10-100 cells) can be easily characterized. Combined with a single cell derived (clonal) sphere formation platform, we have successfully demonstrated the importance of microenvironmental cues for proteolytic activity and also investigated the difference between clones. Furthermore, the platform allows monitoring single cells at multiple time points, unveiling different cancer cell line dynamics in proteolytic activity. The presented tool facilitates single cell proteolytic analysis using small samples, and our findings illuminate the heterogeneous and dynamic nature of proteolytic activity.
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Affiliation(s)
- Yu-Chih Chen
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
- University of Michigan Comprehensive Cancer Center, 1500 E. Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Yu-Heng Cheng
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
| | - Patrick Ingram
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd. Ann Arbor, MI 48109-2099, USA
| | - Euisik Yoon
- Department of Electrical Engineering and Computer Science, University of Michigan, 1301 Beal Avenue, Ann Arbor, MI 48109-2122, USA
- Department of Biomedical Engineering, University of Michigan, 2200 Bonisteel, Blvd. Ann Arbor, MI 48109-2099, USA
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264
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265
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Abstract
Immunoblotting (western blotting) is used to identify specific antigens recognized by polyclonal or monoclonal antibodies. This unit provides protocols for all steps, starting with solubilization of the protein samples, usually by means of SDS and reducing agents. Following solubilization, the material is separated by SDS-PAGE and the antigens are electrophoretically transferred to a membrane, a process that can be monitored by reversible staining with Ponceau S. The transferred proteins are bound to the surface of the membrane, providing access to immunodetection reagents. After nonspecific binding sites are blocked, the membrane is probed with the primary antibody and washed. The antibody-antigen complexes are tagged with fluorophores, horseradish peroxidase, or alkaline phosphatase coupled to a secondary anti-IgG antibody, and detected using appropriate fluorescent imaging technologies or with chromogenic or luminescent substrates. Finally, membranes may be stripped and reprobed.
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Affiliation(s)
| | - Peng Xu
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia
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266
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Redefining Signaling Pathways with an Expanding Single-Cell Toolbox. Trends Biotechnol 2016; 34:458-469. [PMID: 26968612 DOI: 10.1016/j.tibtech.2016.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 02/12/2016] [Accepted: 02/16/2016] [Indexed: 01/12/2023]
Abstract
Genetically identical cells respond heterogeneously to uniform environmental stimuli. Consequently, investigating the signaling networks that control these cell responses using 'average' bulk cell measurements can obscure underlying mechanisms and misses information emerging from cell-to-cell variability. Here we review recent technological advances including live-cell fluorescence imaging-based approaches and microfluidic devices that enable measurements of signaling networks, dynamics, and responses in single cells. We discuss how these single-cell tools have uncovered novel mechanistic insights for canonical signaling pathways that control cell proliferation (ERK), DNA-damage responses (p53), and innate immune and stress responses (NF-κB). Future improvements in throughput and multiplexing, analytical pipelines, and in vivo applicability will all significantly expand the biological information gained from single-cell measurements of signaling pathways.
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267
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de Lange N, Tran TM, Abate AR. Electrical lysis of cells for detergent-free droplet assays. BIOMICROFLUIDICS 2016; 10:024114. [PMID: 27051471 PMCID: PMC4808063 DOI: 10.1063/1.4944742] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 03/13/2016] [Indexed: 05/06/2023]
Abstract
Efficient lysis is critical when analyzing single cells in microfluidic droplets, but existing methods utilize detergents that can interfere with the assays to be performed. We demonstrate robust cell lysis without the use of detergents or other chemicals. In our method, cells are exposed to electric field immediately before encapsulation in droplets, resulting in cell lysis. We characterize lysis efficiency as a function of control parameters and demonstrate compatibility with enzymatic assays by measuring the catalysis of β-glucosidase, an important cellulase used in the conversion of biomass to biofuel. Our method enables assays in microfluidic droplets that are incompatible with detergents.
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Affiliation(s)
| | - T M Tran
- Bioengineering and Therapeutic Sciences, University of California San Francisco , San Francisco, California 14958, USA
| | - A R Abate
- Bioengineering and Therapeutic Sciences, University of California San Francisco , San Francisco, California 14958, USA
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268
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Heath JR, Ribas A, Mischel PS. Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov 2016; 15:204-16. [PMID: 26669673 PMCID: PMC4883669 DOI: 10.1038/nrd.2015.16] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed.
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Affiliation(s)
- James R Heath
- California Institute of Technology Division of Chemistry and Chemical Engineering, MC 127-72, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, California 90095, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research San Diego, Department of Pathology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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269
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Boiani M, Cibelli JB. What we can learn from single-cell analysis in development. Mol Hum Reprod 2016; 22:160-71. [DOI: 10.1093/molehr/gaw014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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270
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Konry T, Sarkar S, Sabhachandani P, Cohen N. Innovative Tools and Technology for Analysis of Single Cells and Cell-Cell Interaction. Annu Rev Biomed Eng 2016; 18:259-84. [PMID: 26928209 DOI: 10.1146/annurev-bioeng-090215-112735] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Heterogeneity in single-cell responses and intercellular interactions results from complex regulation of cell-intrinsic and environmental factors. Single-cell analysis allows not only detection of individual cellular characteristics but also correlation of genetic content with phenotypic traits in the same cell. Technological advances in micro- and nanofabrication have benefited single-cell analysis by allowing precise control of the localized microenvironment, cell manipulation, and sensitive detection capabilities. Additionally, microscale techniques permit rapid, high-throughput, multiparametric screening that has become essential for -omics research. This review highlights innovative applications of microscale platforms in genetic, proteomic, and metabolic detection in single cells; cell sorting strategies; and heterotypic cell-cell interaction. We discuss key design aspects of single-cell localization and isolation in microfluidic systems, dynamic and endpoint analyses, and approaches that integrate highly multiplexed detection of various intracellular species.
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Affiliation(s)
- Tania Konry
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Saheli Sarkar
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Pooja Sabhachandani
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
| | - Noa Cohen
- Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts 02115; , , ,
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271
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Affiliation(s)
- Stephanie M. Schubert
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Stephanie R. Walter
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - Mael Manesse
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | - David R. Walt
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
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272
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Chen D, Fan F, Zhao X, Xu F, Chen P, Wang J, Ban L, Liu Z, Feng X, Zhang Y, Liu BF. Single Cell Chemical Proteomics with Membrane-Permeable Activity-Based Probe for Identification of Functional Proteins in Lysosome of Tumors. Anal Chem 2016; 88:2466-71. [DOI: 10.1021/acs.analchem.5b04645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Dongjuan Chen
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fengkai Fan
- Hubei
Key Laboratory of Purification and Application of Plant Anti-Cancer
Ingredients, College of Chemistry and Life Science, Hubei University of Education, Wuhan, 430205, China
| | - Xingfu Zhao
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fei Xu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Peng Chen
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jie Wang
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lin Ban
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhihua Liu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xiaojun Feng
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yuhui Zhang
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Bi-Feng Liu
- Britton
Chance Center for Biomedical Photonics at Wuhan National Laboratory
for Optoelectronics−Hubei Bioinformatics and Molecular Imaging
Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering,
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
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273
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Duncombe TA, Kang CC, Maity S, Ward TM, Pegram MD, Murthy N, Herr AE. Hydrogel Pore-Size Modulation for Enhanced Single-Cell Western Blotting. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:327-334. [PMID: 26567472 PMCID: PMC4708057 DOI: 10.1002/adma.201503939] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/05/2015] [Indexed: 05/18/2023]
Abstract
Pore-gradient microgel arrays enable thousands of parallel high-resolution single-cell protein electrophoresis separations for targets accross a wide molecular mass (25-289 kDa), yet within 1 mm separation distances. Dual crosslinked hydrogels facilitate gel-pore expansion after electrophoresis for efficient and uniform immunoprobing. The photopatterned, light-activated, and acid-expandable hydrogel underpins single-cell protein analysis, here for oncoprotein-related signaling in human breast biopsy.
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Affiliation(s)
- Todd A. Duncombe
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Chi-Chih Kang
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Santanu Maity
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
| | - Toby M. Ward
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, CA 94305, USA
| | - Mark D. Pegram
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, CA 94305, USA
| | - Niren Murthy
- Department of Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California, CA 94720, USA
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274
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Affiliation(s)
- Sanjin Hosic
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
| | - Shashi K. Murthy
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA, USA
| | - Abigail N. Koppes
- Department of Chemical Engineering, Northeastern University, Boston, MA, USA
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275
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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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276
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Li Y, Ye T, Yang F, Hu M, Liang L, He H, Li Z, Zeng A, Li Y, Yao Y, Xie Y, An Z, Li S. Punica granatum (pomegranate) peel extract exerts potent antitumor and anti-metastasis activity in thyroid cancer. RSC Adv 2016. [DOI: 10.1039/c6ra13167k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The incidence of thyroid carcinoma has obviously been rising throughout the world during the past ten years.
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277
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Novo P, Dell'Aica M, Janasek D, Zahedi RP. High spatial and temporal resolution cell manipulation techniques in microchannels. Analyst 2016; 141:1888-905. [DOI: 10.1039/c6an00027d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Reviewing latest developments on lab on chips for enhanced control of cells’ experiments.
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Affiliation(s)
- Pedro Novo
- Protein Dynamics Group
- Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V
- 44227 Dortmund
- Germany
| | - Margherita Dell'Aica
- Protein Dynamics Group
- Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V
- 44227 Dortmund
- Germany
| | - Dirk Janasek
- Protein Dynamics Group
- Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V
- 44227 Dortmund
- Germany
| | - René P. Zahedi
- Protein Dynamics Group
- Leibniz-Institut für Analytische Wissenschaften – ISAS - e.V
- 44227 Dortmund
- Germany
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278
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Affiliation(s)
- Michael G. Roper
- Department of Chemistry and
Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
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279
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Huang L, Chen Y, Chen Y, Wu H. Centrifugation-Assisted Single-Cell Trapping in a Truncated Cone-Shaped Microwell Array Chip for the Real-Time Observation of Cellular Apoptosis. Anal Chem 2015; 87:12169-76. [DOI: 10.1021/acs.analchem.5b03031] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lu Huang
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
- Division of Biomedical
Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yin Chen
- Division of Biomedical
Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Yangfan Chen
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hongkai Wu
- Department of Chemistry, The Hong Kong University of Science and Technology, Hong Kong, China
- Division of Biomedical
Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
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280
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Abstract
INTRODUCTION The past decade has witnessed tremendous progress in surface micropatterning techniques for generating arrays of various types of biomolecules. Multiplexed protein micropatterning has tremendous potential for drug discovery providing versatile means for high throughput assays required for target and lead identification as well as diagnostics and functional screening for personalized medicine. However, ensuring the functional integrity of proteins on surfaces has remained challenging, in particular in the case of membrane proteins, the most important class of drug targets. Yet, generic strategies to control functional organization of proteins into micropatterns are emerging. AREAS COVERED This review includes an overview introducing the most common approaches for surface modification and functional protein immobilization. The authors present the key photo and soft lithography techniques with respect to compatibility with functional protein micropatterning and multiplexing capabilities. In the second part, the authors present the key applications of protein micropatterning techniques in drug discovery with a focus on membrane protein interactions and cellular signaling. EXPERT OPINION With the growing importance of target discovery as well as protein-based therapeutics and personalized medicine, the application of protein arrays can play a fundamental role in drug discovery. Yet, important technical breakthroughs are still required for broad application of these approaches, which will include in vitro "copying" of proteins from cDNA arrays into micropatterns, direct protein capturing from single cells as well as protein microarrays in living cells.
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Affiliation(s)
- Changjiang You
- a Department of Biology, Division of Biophysics , University of Osnabrück , Osnabrück 49076 , Germany
| | - Jacob Piehler
- a Department of Biology, Division of Biophysics , University of Osnabrück , Osnabrück 49076 , Germany
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281
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Choi H, Choi N, Lim B, Kim TW, Song S, Kim YP. Sequential phosphorylation analysis using dye-tethered peptides and microfluidic isoelectric focusing electrophoresis. Biosens Bioelectron 2015; 73:93-99. [PMID: 26050965 DOI: 10.1016/j.bios.2015.05.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/11/2015] [Accepted: 05/21/2015] [Indexed: 11/25/2022]
Abstract
We report a simple method for analyzing sequential phosphorylation by protein kinases using fluorescent peptide substrates and microfluidic isoelectric focusing (μIEF) electrophoresis. When a dye-labeled peptide substrate was sequentially phosphorylated by two consecutive protein kinases (mitogen-activated protein kinase (MAPK) and glycogen synthase kinase 3 (GSK3)), its differently phosphorylated forms were easily separated and visualized by fluorescent focusing zones in the μIEF channel based on a change in the isoelectric point (pI) by phosphorylation. As a result, ratiometric and quantitative analysis of the fluorescent focusing regions shifted by phosphorylation enabled the analysis of phosphorylation efficiency and the relevant inhibition of protein kinases (MAPK and GSK3) with high simplicity and selectivity. Furthermore, the GSK3 activity in the cell lysates was elucidated by μIEF electrophoresis in combination with immunoprecipitation. Our results suggest that this method has great potential for analyzing the sequential phosphorylation of multiple protein kinases that are implicated in cellular signaling pathways.
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Affiliation(s)
- Hoseok Choi
- Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Nakchul Choi
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul 133-791, Republic of Korea
| | - Butaek Lim
- Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Tae-Wuk Kim
- Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea
| | - Simon Song
- Department of Mechanical Convergence Engineering, Hanyang University, Seoul 133-791, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 133-791, Republic of Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 133-791, Republic of Korea; Research Institute for Natural Sciences, Hanyang University, Seoul 133-791, Republic of Korea; Institute of Nano Science and Technology, Hanyang University, Seoul 133-791, Republic of Korea.
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282
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Abstract
The underlying physical properties of microfluidic tools have led to new biological insights through the development of microsystems that can manipulate, mimic and measure biology at a resolution that has not been possible with macroscale tools. Microsystems readily handle sub-microlitre volumes, precisely route predictable laminar fluid flows and match both perturbations and measurements to the length scales and timescales of biological systems. The advent of fabrication techniques that do not require highly specialized engineering facilities is fuelling the broad dissemination of microfluidic systems and their adaptation to specific biological questions. We describe how our understanding of molecular and cell biology is being and will continue to be advanced by precision microfluidic approaches and posit that microfluidic tools - in conjunction with advanced imaging, bioinformatics and molecular biology approaches - will transform biology into a precision science.
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283
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Wade J, Alsop AT, Vertin NR, Yang H, Johnson MD, Bailey RC. Rapid, Multiplexed Phosphoprotein Profiling Using Silicon Photonic Sensor Arrays. ACS CENTRAL SCIENCE 2015; 1:374-382. [PMID: 26539563 PMCID: PMC4626792 DOI: 10.1021/acscentsci.5b00250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Indexed: 05/04/2023]
Abstract
Extracellular signaling is commonly mediated through post-translational protein modifications that propagate messages from membrane-bound receptors to ultimately regulate gene expression. Signaling cascades are ubiquitously intertwined, and a full understanding of function can only be gleaned by observing dynamics across multiple key signaling nodes. Importantly, targets within signaling cascades often represent opportunities for therapeutic development or can serve as diagnostic biomarkers. Protein phosphorylation is a particularly important post-translational modification that controls many essential cellular signaling pathways. Not surprisingly, aberrant phosphorylation is found in many human diseases, including cancer, and phosphoprotein-based biomarker signatures hold unrealized promise for disease monitoring. Moreover, phosphoprotein analysis has wide-ranging applications across fundamental chemical biology, as many drug discovery efforts seek to target nodes within kinase signaling pathways. For both fundamental and translational applications, the analysis of phosphoprotein biomarker targets is limited by a reliance on labor-intensive and/or technically challenging methods, particularly when considering the simultaneous monitoring of multiplexed panels of phosphoprotein biomarkers. We have developed a technology based upon arrays of silicon photonic microring resonator sensors that fills this void, facilitating the rapid and automated analysis of multiple phosphoprotein levels from both cell lines and primary human tumor samples requiring only minimal sample preparation.
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Affiliation(s)
- James
H. Wade
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Aurora T. Alsop
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Nicholas R. Vertin
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Hongwei Yang
- Department
of Neurological Surgery, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mark D. Johnson
- Department
of Neurological Surgery, Brigham and Women’s
Hospital and Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Ryan C. Bailey
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
- E-mail:
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284
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Landry BD, Clarke DC, Lee MJ. Studying Cellular Signal Transduction with OMIC Technologies. J Mol Biol 2015; 427:3416-40. [PMID: 26244521 PMCID: PMC4818567 DOI: 10.1016/j.jmb.2015.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 07/25/2015] [Accepted: 07/27/2015] [Indexed: 11/24/2022]
Abstract
In the gulf between genotype and phenotype exists proteins and, in particular, protein signal transduction systems. These systems use a relatively limited parts list to respond to a much longer list of extracellular, environmental, and/or mechanical cues with rapidity and specificity. Most signaling networks function in a highly non-linear and often contextual manner. Furthermore, these processes occur dynamically across space and time. Because of these complexities, systems and "OMIC" approaches are essential for the study of signal transduction. One challenge in using OMIC-scale approaches to study signaling is that the "signal" can take different forms in different situations. Signals are encoded in diverse ways such as protein-protein interactions, enzyme activities, localizations, or post-translational modifications to proteins. Furthermore, in some cases, signals may be encoded only in the dynamics, duration, or rates of change of these features. Accordingly, systems-level analyses of signaling may need to integrate multiple experimental and/or computational approaches. As the field has progressed, the non-triviality of integrating experimental and computational analyses has become apparent. Successful use of OMIC methods to study signaling will require the "right" experiments and the "right" modeling approaches, and it is critical to consider both in the design phase of the project. In this review, we discuss common OMIC and modeling approaches for studying signaling, emphasizing the philosophical and practical considerations for effectively merging these two types of approaches to maximize the probability of obtaining reliable and novel insights into signaling biology.
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Affiliation(s)
- Benjamin D Landry
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - David C Clarke
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6 Canada
| | - Michael J Lee
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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285
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Abstract
Applications as diverse as drug delivery and immunoassays require hydrogels to house high concentration macromolecular solutions. Yet, thermodynamic partitioning acts to lower the equilibrium concentration of macromolecules in the hydrogel, as compared to the surrounding liquid phase. For immunoassays that utilize a target antigen immobilized in the hydrogel, partitioning hinders introduction of detection antibody into the gel and, consequently, reduces the in-gel concentration of detection antibody, adversely impacting assay sensitivity. Recently, we developed a single-cell targeted proteomic assay with polyacrylamide gel electrophoresis of single cell lysates followed by an in-gel immunoassay. In the present work, we overcome partitioning that both limits analytical sensitivity and increases consumption of costly detection antibody by performing the immunoassay step after dehydrating the antigen-containing polyacrylamide gel. Gels are rehydrated with a solution of detection antibody. We hypothesized that matching the volume of detection antibody solution with the hydrogel water volume fraction would ensure that, at equilibrium, the detection antibody mass resides in the gel and not in the liquid surrounding the gel. Using this approach, we observe (compared with antibody incubation of hydrated gels): (i) 4-11 fold higher concentration of antibody in the dehydrated gels and in the single-cell assay (ii) higher fluorescence immunoassay signal, with up to 5-fold increases in signal-to-noise-ratio and (iii) reduced detection antibody consumption. We also find that detection antibody signal may be less well-correlated with target protein levels (GFP) using this method, suggesting a trade-off between analytical sensitivity and variation in immunoprobe signal. Our volume-matching approach for introducing macromolecular solutions to hydrogels increases the local in-gel concentration of detection antibody without requiring modification of the hydrogel structure, and thus we anticipate broad applicability to hydrogel-based assays, diagnostics, and drug delivery.
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Affiliation(s)
- Julea Vlassakis
- Department of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley , Berkeley, California 94720, United States
| | - Amy E Herr
- Department of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley , Berkeley, California 94720, United States
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286
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Abbaspourrad A, Zhang H, Tao Y, Cui N, Asahara H, Zhou Y, Yue D, Koehler SA, Ung LW, Heyman J, Ren Y, Ziblat R, Chong S, Weitz DA. Label-free single-cell protein quantification using a drop-based mix-and-read system. Sci Rep 2015; 5:12756. [PMID: 26234416 PMCID: PMC4522677 DOI: 10.1038/srep12756] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/22/2015] [Indexed: 12/14/2022] Open
Abstract
Quantitative protein analysis of single cells is rarely achieved due to technical difficulties of detecting minute amounts of proteins present in one cell. We develop a mix-and-read assay for drop-based label-free protein analysis of single cells. This high-throughput method quantifies absolute, rather than relative, amounts of proteins and does not involve antibody labeling or mass spectrometry.
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Affiliation(s)
- Alireza Abbaspourrad
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Huidan Zhang
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Cell Biology, Key Laboratory of Cell Biology, Ministry of Public Health, and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang 110001, China
| | - Ye Tao
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Naiwen Cui
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Haruichi Asahara
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Ying Zhou
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Dongxian Yue
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Stephan A Koehler
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Lloyd W Ung
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - John Heyman
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Yukun Ren
- School of Mechatronics Engineering, Harbin Institute of Technology, Harbin 150001, China
| | - Roy Ziblat
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Shaorong Chong
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - David A Weitz
- 1] School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA [2] Department of Physics, Harvard University, Cambridge, MA 02138, USA
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287
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Dittrich P, Ibáñez AJ. Analysis of metabolites in single cells-what is the best micro-platform? Electrophoresis 2015; 36:2196-2206. [PMID: 25929796 DOI: 10.1002/elps.201500045] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 04/04/2015] [Accepted: 04/04/2015] [Indexed: 11/11/2022]
Abstract
This review covers new innovations and developments in the field of single-cell level analysis of metabolites, involving the role of microfluidic and microarray platforms to manipulate and handle the cells prior their detection. Microfluidic and microarray platforms have shown great promise. The latest developments demonstrate their potential to identify a particular cell or even an ensemble of cells (sharing a common property or phenotype) that co-exist in a much larger cell population. The reason for this is the capability of these platforms to perform several complex analytical processes, such as: cleanup, sorting, derivatization, separation, and detection, with great robustness, speed, and reduced sample/reagent consumption. Here, we present several examples that illustrate the rapid strides that have been made for the routine analysis of metabolites by coupling different microfluidics and microarrays devices to a wide range of analytical detectors (e.g. fluorescent microscopy, electrochemical, and mass spectrometry). Herein, we also present selected examples detailing the use of microfluidics and microarrays in the visualization of the natural occurring cell-to-cell heterogeneity in isogenic populations, in particular during the response to external cues. The possibility to accurate monitor the cell-to-cell heterogeneity based on different levels of key metabolites is of clinical relevance, since cell-to-cell heterogeneity can influence, for example, the outcome of a drug treatment.
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Affiliation(s)
- Petra Dittrich
- ETH Zurich - Chemie und Angewandte Biowissenschaften, Wolfgang-Pauli-Str. 10, Zurich, 8093, Switzerland
| | - Alfredo J Ibáñez
- ETH Zurich - Department of Chemistry and Applied Biosciences, Vladimir-Prelog-weg 3, Zurich, 8093, Switzerland
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288
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Wedeking T, Löchte S, Richter CP, Bhagawati M, Piehler J, You C. Single Cell GFP-Trap Reveals Stoichiometry and Dynamics of Cytosolic Protein Complexes. NANO LETTERS 2015; 15:3610-3615. [PMID: 25901412 DOI: 10.1021/acs.nanolett.5b01153] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We developed in situ single cell pull-down (SiCPull) of GFP-tagged protein complexes based on micropatterned functionalized surface architectures. Cells cultured on these supports are lysed by mild detergents and protein complexes captured to the surface are probed in situ by total internal reflection fluorescence microscopy. Using SiCPull, we quantitatively mapped the lifetimes of various signal transducer and activator of transcription complexes by monitoring dissociation from the surface and defined their stoichiometry on the single molecule level.
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Affiliation(s)
- Tim Wedeking
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | | | - Maniraj Bhagawati
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
| | - Changjiang You
- Department of Biology, University of Osnabrück, 49076 Osnabrück, Germany
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289
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Higuchi A, Wang CT, Ling QD, Lee HHC, Kumar SS, Chang Y, Alarfaj AA, Munusamy MA, Hsu ST, Wu GJ, Umezawa A. A hybrid-membrane migration method to isolate high-purity adipose-derived stem cells from fat tissues. Sci Rep 2015; 5:10217. [PMID: 25970301 PMCID: PMC4429558 DOI: 10.1038/srep10217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/02/2015] [Indexed: 01/03/2023] Open
Abstract
Human adipose-derived stem cells (hADSCs) exhibit heterogeneous characteristics, indicating various genotypes and differentiation abilities. The isolated hADSCs can possess different purity levels and divergent properties depending on the purification methods used. We developed a hybrid-membrane migration method that purifies hADSCs from a fat tissue solution with extremely high purity and pluripotency. A primary fat-tissue solution was permeated through the porous membranes with a pore size from 8 to 25 μm, and the membranes were incubated in cell culture medium for 15-18 days. The hADSCs that migrated from the membranes contained an extremely high percentage (e.g., >98%) of cells positive for mesenchymal stem cell markers and showed almost one order of magnitude higher expression of some pluripotency genes (Oct4, Sox2, Klf4 and Nanog) compared with cells isolated using the conventional culture method.
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Affiliation(s)
- Akon Higuchi
- 1] Department of Chemical and Materials Engineering, National Central University, Jhong-li, Taoyuan, Taiwan [2] Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia [3] Department of Reproduction, National Research Institute for Child Health and Development, Tokyo, Japan [4] Nano Medical Engineering Laboratory, RIKEN, Wako, Saitama, Japan
| | - Ching-Tang Wang
- Department of Chemical and Materials Engineering, National Central University, Jhong-li, Taoyuan, Taiwan
| | - Qing-Dong Ling
- 1] Institute of Systems Biology and Bioinformatics, National Central University, Jhong-li, Taoyuan, Taiwan [2] Cathay Medical Research Institute, Cathay General Hospital, Taipei, Taiwan
| | | | - S Suresh Kumar
- Department of Medical Microbiology and Parasitology, Universities Putra Malaysia, Slangor, Malaysia
| | - Yung Chang
- Department of Chemical Engineering, R&D Center for Membrane Technology, Chung Yuan Christian University, Jhong-li, Taoyuan, Taiwan
| | - Abdullah A Alarfaj
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Murugan A Munusamy
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Shih-Tien Hsu
- Department of Internal Medicine, Taiwan Landseed Hospital, Pingjen, Taoyuan, Taiwan
| | - Gwo-Jang Wu
- Graduate Institute of Medical Sciences and Department of Obstetrics &Gynecology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Akihiko Umezawa
- Department of Reproduction, National Research Institute for Child Health and Development, Tokyo, Japan
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290
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Yang HJ, Ratnapriya R, Cogliati T, Kim JW, Swaroop A. Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease. Prog Retin Eye Res 2015; 46:1-30. [PMID: 25668385 PMCID: PMC4402139 DOI: 10.1016/j.preteyeres.2015.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/18/2015] [Accepted: 01/21/2015] [Indexed: 01/10/2023]
Abstract
Genomics and genetics have invaded all aspects of biology and medicine, opening uncharted territory for scientific exploration. The definition of "gene" itself has become ambiguous, and the central dogma is continuously being revised and expanded. Computational biology and computational medicine are no longer intellectual domains of the chosen few. Next generation sequencing (NGS) technology, together with novel methods of pattern recognition and network analyses, has revolutionized the way we think about fundamental biological mechanisms and cellular pathways. In this review, we discuss NGS-based genome-wide approaches that can provide deeper insights into retinal development, aging and disease pathogenesis. We first focus on gene regulatory networks (GRNs) that govern the differentiation of retinal photoreceptors and modulate adaptive response during aging. Then, we discuss NGS technology in the context of retinal disease and develop a vision for therapies based on network biology. We should emphasize that basic strategies for network construction and analyses can be transported to any tissue or cell type. We believe that specific and uniform guidelines are required for generation of genome, transcriptome and epigenome data to facilitate comparative analysis and integration of multi-dimensional data sets, and for constructing networks underlying complex biological processes. As cellular homeostasis and organismal survival are dependent on gene-gene and gene-environment interactions, we believe that network-based biology will provide the foundation for deciphering disease mechanisms and discovering novel drug targets for retinal neurodegenerative diseases.
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Affiliation(s)
- Hyun-Jin Yang
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Tiziana Cogliati
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Jung-Woong Kim
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, 6 Center Drive, Bethesda, MD 20892-0610, USA.
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291
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Göttgens B. Regulatory network control of blood stem cells. Blood 2015; 125:2614-20. [PMID: 25762179 DOI: 10.1182/blood-2014-08-570226] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 10/06/2014] [Indexed: 12/13/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are characterized by their ability to execute a wide range of cell fate choices, including self-renewal, quiescence, and differentiation into the many different mature blood lineages. Cell fate decision making in HSCs, as indeed in other cell types, is driven by the interplay of external stimuli and intracellular regulatory programs. Given the pivotal nature of HSC decision making for both normal and aberrant hematopoiesis, substantial research efforts have been invested over the last few decades into deciphering some of the underlying mechanisms. Central to the intracellular decision making processes are transcription factor proteins and their interactions within gene regulatory networks. More than 50 transcription factors have been shown to affect the functionality of HSCs. However, much remains to be learned about the way in which individual factors are connected within wider regulatory networks, and how the topology of HSC regulatory networks might affect HSC function. Nevertheless, important progress has been made in recent years, and new emerging technologies suggest that the pace of progress is likely to accelerate. This review will introduce key concepts, provide an integrated view of selected recent studies, and conclude with an outlook on possible future directions for this field.
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Affiliation(s)
- Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust & Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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292
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Pagaduan JV, Sahore V, Woolley AT. Applications of microfluidics and microchip electrophoresis for potential clinical biomarker analysis. Anal Bioanal Chem 2015; 407:6911-22. [PMID: 25855148 DOI: 10.1007/s00216-015-8622-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/20/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
Abstract
This article reviews advances over the last five years in microfluidics and microchip-electrophoresis techniques for detection of clinical biomarkers. The variety of advantages of miniaturization compared with conventional benchtop methods for detecting biomarkers has resulted in increased interest in developing cheap, fast, and sensitive techniques. We discuss the development of applications of microfluidics and microchip electrophoresis for analysis of different clinical samples for pathogen identification, personalized medicine, and biomarker detection. We emphasize the advantages of microfluidic techniques over conventional methods, which make them attractive future diagnostic tools. We also discuss the versatility and adaptability of this technology for analysis of a variety of biomarkers, including lipids, small molecules, carbohydrates, nucleic acids, proteins, and cells. Finally, we conclude with a discussion of aspects that need to be improved to move this technology towards routine clinical and point-of-care applications.
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Affiliation(s)
- Jayson V Pagaduan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, USA
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293
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294
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Blazek M, Santisteban TS, Zengerle R, Meier M. Analysis of fast protein phosphorylation kinetics in single cells on a microfluidic chip. LAB ON A CHIP 2015; 15:726-734. [PMID: 25428717 DOI: 10.1039/c4lc00797b] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In the present study, we developed a microfluidic large-scale integration (mLSI) platform for the temporal and chemical control of cell cultures to study fast kinetics of protein phosphorylation. For in situ protein analysis the mLSI chip integrates the Proximity Ligation Assay (PLA). To investigate cell-signaling events with a time resolution of a few seconds we first engineered and optimized the fluidic layout of the chip with 128 individual addressable cell culture chambers. The functionality of the cell culture operations and PLA is demonstrated by the determination of the minimum cell sample size for obtaining robust quantitative PLA signals at the single-cell level. We show that at least 350 cells per assay condition are required to statistically evaluate single cell PLA data. In the following we used the PLA chip with over 500 hundred cells per condition to record sequential phosphorylation reactions of the canonical protein kinase within the Akt pathway, which is activated in various human cancer types. This was achieved by stimulating mouse fibroblast cell cultures with either the platelet-derived growth factor (PDGF) or insulin-like growth factor (IGF-1). Fluidic cell stimulation pulses of 5 seconds were followed by precisely time shifted cell fixation pulses to obtain a temporal resolution of 10 seconds. PLA was then performed on all fixed arrays of cell cultures to extract the characteristic phosphorylation times at the single cell level for either the PDGF, or IGF-1 receptor and the Akt and GSK3β kinases. Characteristic phosphorylation times for the receptors were between 13 and 35 seconds, whereas for downstream kinases between 25 and 200 seconds. Thus we could reveal a molecular order of the phosphorylation reactions during the signal transduction through the Akt pathway. In dependence of the stimulus we found a temporal difference for the characteristic phosphorylation time of 20 and 150 seconds for the Ser-473 and Thr-308 residues on the Akt kinase, respectively. Temporal alteration of sequential phosphorylation reactions on Akt has been proposed as molecular mechanism to differentiate between stimuli and biophysically determined in the present study.
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Affiliation(s)
- Matthias Blazek
- Microfluidic and Biological Engineering, Department of Microsystems Engineering - IMTEK, University of Freiburg, Georges-Koehler-Allee 103, 79110 Freiburg, Germany.
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295
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Salehi-Reyhani A, Gesellchen F, Mampallil D, Wilson R, Reboud J, Ces O, Willison KR, Cooper JM, Klug DR. Chemical-Free Lysis and Fractionation of Cells by Use of Surface Acoustic Waves for Sensitive Protein Assays. Anal Chem 2015; 87:2161-9. [DOI: 10.1021/ac5033758] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
| | - Frank Gesellchen
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Dileep Mampallil
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Rab Wilson
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | - Julien Reboud
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
| | | | | | - Jonathan M. Cooper
- Division
of Biomedical Engineering, School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow G12 8LT, United Kingdom
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296
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Abstract
Cell heterogeneity is a variation in cellular processes in functionally similar cells. Cells from the same tissue which are considered genetically identical may have difference in size, structure, and level of protein expression which can lead to major impact on the functions of cell leading to difference in physiological consequences. Single-cell proteome-wide studies are used to detect cell heterogeneity. Flow cytometry and immunocytochemistry do play an important role in evaluating cell heterogeneity. However, these methods are based on separation by antibodies with limited specificity. Cross-reactivity can occur leading to bias in result. Western blot is done to separate the proteins according to molecular weight. Therefore, off-target and on-target signals can be discriminated. Detection of protein expression from a tissue can be done with the help of western blot. However, it is unable to differentiate protein expression of individual cells. For detection of this cell-to-cell variation, a highly advanced technique termed "single-cell western blotting" is carried out. Single-cell western blot has enabled us to detect protein expression at cellular level at a fairly advanced high resolution using a western blot designed to assess cell heterogeneity.
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297
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Abstract
Little headway has been made in single cell protein analysis, aside from tools that rely solely on antibody-probe based detection (i.e., flow cytometry, immunocytochemistry), which are limited by low specificity and multiplexing capabilities. To address these protein analysis gaps, we have introduced a single-cell western blot (scWestern). The protein assay is capable of highly specific analysis by coupling antibody-based detection with a polyacrylamide gel electrophoresis (PAGE) protein separation. Cells are settled via gravity into polyacrylamide (PA) microwells, chemically lysed in the wells, and then subjected to PAGE through the walls of the microwells and into the surrounding PA gel. Over a thousand single-cell separations are performed simultaneously, and multiple protein targets of interest are investigated. After PAGE separation, photo-immobilization of all proteins to the gel allows for antibody probing and lends to the archival quality of the scWestern assay where new proteins targets can be investigated months after the initial separations are performed.
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Affiliation(s)
- Elly Sinkala
- Department of Bioengineering, University of California Berkeley, 306 Stanley Hall MC 1762, Berkeley, CA, 94720-1762, USA
| | - Amy E Herr
- Department of Bioengineering, University of California Berkeley, 306 Stanley Hall MC 1762, Berkeley, CA, 94720-1762, USA.
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298
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Ortega AD, Quereda JJ, Pucciarelli MG, García-del Portillo F. Non-coding RNA regulation in pathogenic bacteria located inside eukaryotic cells. Front Cell Infect Microbiol 2014; 4:162. [PMID: 25429360 PMCID: PMC4228915 DOI: 10.3389/fcimb.2014.00162] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 10/20/2014] [Indexed: 01/06/2023] Open
Abstract
Intracellular bacterial pathogens have evolved distinct lifestyles inside eukaryotic cells. Some pathogens coexist with the infected cell in an obligate intracellular state, whereas others transit between the extracellular and intracellular environment. Adaptation to these intracellular lifestyles is regulated in both space and time. Non-coding small RNAs (sRNAs) are post-transcriptional regulatory molecules that fine-tune important processes in bacterial physiology including cell envelope architecture, intermediate metabolism, bacterial communication, biofilm formation, and virulence. Recent studies have shown production of defined sRNA species by intracellular bacteria located inside eukaryotic cells. The molecules targeted by these sRNAs and their expression dynamics along the intracellular infection cycle remain, however, poorly characterized. Technical difficulties linked to the isolation of “intact” intracellular bacteria from infected host cells might explain why sRNA regulation in these specialized pathogens is still a largely unexplored field. Transition from the extracellular to the intracellular lifestyle provides an ideal scenario in which regulatory sRNAs are intended to participate; so much work must be done in this direction. This review focuses on sRNAs expressed by intracellular bacterial pathogens during the infection of eukaryotic cells, strategies used with these pathogens to identify sRNAs required for virulence, and the experimental technical challenges associated to this type of studies. We also discuss varied techniques for their potential application to study RNA regulation in intracellular bacterial infections.
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Affiliation(s)
- Alvaro D Ortega
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain
| | - Juan J Quereda
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain
| | - M Graciela Pucciarelli
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC) Madrid, Spain ; Departamento de Biología Molecular, Universidad Autónoma de Madrid, Centro de Biología Molecular 'Severo Ochoa' (CBMSO-CSIC) Madrid, Spain
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299
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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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300
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Kang CC, Lin JM, Xu Z, Kumar S, Herr AE. Single-cell Western blotting after whole-cell imaging to assess cancer chemotherapeutic response. Anal Chem 2014; 86:10429-36. [PMID: 25226230 PMCID: PMC4204918 DOI: 10.1021/ac502932t] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 09/16/2014] [Indexed: 12/12/2022]
Abstract
Intratumor heterogeneity remains a major obstacle to effective cancer therapy and personalized medicine. Current understanding points to differential therapeutic response among subpopulations of tumor cells as a key challenge to successful treatment. To advance our understanding of how this heterogeneity is reflected in cell-to-cell variations in chemosensitivity and expression of drug-resistance proteins, we optimize and apply a new targeted proteomics modality, single-cell western blotting (scWestern), to a human glioblastoma cell line. To acquire both phenotypic and proteomic data on the same, single glioblastoma cells, we integrate high-content imaging prior to the scWestern assays. The scWestern technique supports thousands of concurrent single-cell western blots, with each assay comprised of chemical lysis of single cells seated in microwells, protein electrophoresis from those microwells into a supporting polyacrylamide (PA) gel layer, and in-gel antibody probing. We systematically optimize chemical lysis and subsequent polyacrylamide gel electrophoresis (PAGE) of the single-cell lysate. The scWestern slides are stored for months then reprobed, thus allowing archiving and later analysis as relevant to sparingly limited, longitudinal cell specimens. Imaging and scWestern analysis of single glioblastoma cells dosed with the chemotherapeutic daunomycin showed both apoptotic (cleaved caspase 8- and annexin V-positive) and living cells. Intriguingly, living glioblastoma subpopulations show up-regulation of a multidrug resistant protein, P-glycoprotein (P-gp), suggesting an active drug efflux pump as a potential mechanism of drug resistance. Accordingly, linking of phenotype with targeted protein analysis with single-cell resolution may advance our understanding of drug response in inherently heterogeneous cell populations, such as those anticipated in tumors.
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Affiliation(s)
- Chi-Chih Kang
- Department
of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Jung-Ming
G. Lin
- Department
of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Zhuchen Xu
- Department
of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Sanjay Kumar
- Department
of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Amy E. Herr
- Department
of Bioengineering and The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
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